Peptide fragments from filoviruses and their uses

ABSTRACT

Isolated peptides comprising one or more antigenic sites of filovirus glycoprotein and methods of their use and production are disclosed. Nucleic acid molecules encoding the peptides are also provided. In several embodiments, the peptides can be used to induce an immune response to filovirus glycoprotein, such as Zaire ebolavirus glycoprotein, in a subject, for example, to treat or prevent infection of the subject with the virus.

CROSS REFERENCE TO RELATED APPLICATIONS

This is the U.S. National Stage of International Application No. PCT/US2017/059407, filed Oct. 31, 2017, which was published in English under PCT Article 21(2), which in turn claims the benefit of U.S. Provisional Application No. 62/414,960, filed Oct. 31, 2016. The provisional application is incorporated herein by reference in its entirety.

FIELD

The present disclosure relates to immunogenic compositions comprising one or more peptide fragments from filoviruses that can induce an immune response in a mammal.

BACKGROUND

The 2014 epidemic of highly pathogenic ebolavirus in Western Africa resulted in tens of thousands of infections and deaths. With occasional small outbreaks of new cases in West Africa and the possibility of long-term persistence of virus in some survivors, it is feared that future outbreaks can occur, resulting in severe epidemics. Development of an effective vaccine against ebolavirus is a high priority, both for pre-epidemic preparedness and for rapid vaccination to control future outbreaks.

Protection against Ebola Virus Disease is, at least, partially attributed to the humoral immune response, since passive transfer of antibodies to naïve non-human primates can protect the recipients against lethal ebolavirus challenge. However, no single assay has been found to be predictive of protection while the correlation of antibody titers measured by various assays has not been clearly demonstrated. Further, the difficulty of conducting adequate randomized controlled trials to demonstrate vaccine effectiveness impedes vaccine development.

SUMMARY

Disclosed herein are isolated peptide fragments of filovirus glycoprotein (GP) that induce an immune response to the GP that neutralizes infection by the virus. The peptide fragments include an identified antigenic site of the filovirus GP that is capable of inducing a neutralizing immune response in a subject. Accordingly, isolated peptides are provided that contain a disclosed filovirus GP antigenic site. In some embodiments, the isolated peptide is from an ebolavirus GP and induces an immune response to ebolavirus GP that neutralizes subsequent infection with the ebolavirus. The peptide can be further conjugated to a carrier to facilitate presentation to the immune system.

In some embodiments, an isolated peptide is provided, wherein the peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as the antigenic site VI of a filovirus GP, such as SEQ ID NO: 9: KNITDKIX₁QIIHDFX₂DX₃X₄LPX₅QX₆X₇X₈X₉NWW, wherein X₁ is D or N, X₂ is V or I, X₃ is K or N, X₄ is T, P, or N, X₅ is D or N, X₆ is G, T, D, or N, X₇ is D or N, X₈ is N, D, or G, and X₉ is D or S, wherein the peptide is no more than 100 (such as no more than 75 or no more than 50) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. For example, an isolated peptide comprising, consisting essentially of, or consisting of the amino acid sequence set forth any one of SEQ ID NOs: 10-13 or 53 or 4, 14-16, or 54.

In some embodiments, an isolated peptide is provided, wherein the peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as the antigenic site VIA of a filovirus GP, such as SEQ ID NO: 6: FX₂DX₃X₄LPX₅QX₆X₇X₈X₉NWWT, wherein X₂ is V or I, X₃ is K or N, X₄ is T, P, or N, X₅ is D or N; X₆ is G, T, D, or N; X₇ is D or N, X₈ is N, D, or G; and X₉ is D or S, wherein the peptide is no more than 100 (such as no more than 75 or no more than 50) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. For example, an isolated peptide comprising, consisting essentially of, or consisting of the amino acid sequence set forth as any one of SEQ ID NO: 5 or residues 14-30 of any one of SEQ ID NOs: 14-16 or 54.

In some embodiments, an isolated peptide is provided, wherein the peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as the antigenic site V.7 of a filovirus GP, such as any one of SEQ ID NOs: 3, 32-34, or 55, wherein the peptide is no more than 100 (such as no more than 75 or no more than 50) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject.

In some embodiments, an isolated peptide is provided, wherein the peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as the antigenic site V.6 of a filovirus GP, such as any one of SEQ ID NOs: 2, 26-28, or 56, or 43-46 or 57, wherein the peptide is no more than 100 (such as no more than 75 or no more than 50) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject.

In some embodiments, an isolated peptide is provided, wherein the peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as the antigenic site IV.1 of a filovirus GP, such as any one of SEQ ID NOs: 17-20 or 58, wherein the peptide is no more than 100 (such as no more than 75 or no more than 50) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject.

In some embodiments, an isolated peptide is provided, wherein the peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as the antigenic site V.1 of a filovirus GP, such as any one of SEQ ID NOs: 21-25 or 59, wherein the peptide is no more than 100 (such as no more than 75 or no more than 50) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject.

In some embodiments, an isolated peptide is provided, wherein the peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as the antigenic site V.10 of a filovirus GP, such as any one of SEQ ID NOs: 29-31 or 60, wherein the peptide is no more than 100 (such as no more than 75 or no more than 50) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject.

In some embodiments, an isolated peptide is provided, wherein the peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as the antigenic site II.1 of a filovirus GP, such as any one of SEQ ID NOs: 47-50 or 61, wherein the peptide is no more than 100 (such as no more than 75 or no more than 50) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject.

In some embodiments, an isolated peptide is provided, wherein the peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as the antigenic site IV.2 of a filovirus GP, such as any one of SEQ ID NOs: 51-52 or 62, wherein the peptide is no more than 100 (such as no more than 75 or no more than 50) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject.

Nucleic acid molecules encoding the disclosed immunogens and expression vectors (such as an inactivated or attenuated viral vector) including the nucleic acid molecules are also provided.

Immunogenic compositions including the disclosed peptide (for example, linked to a carrier) or a nucleic acid molecule or vector encoding the peptide are also provided. The immunogenic composition is suitable for administration to a subject, and may also be contained in a unit dosage form. The immunogenic compositions can further include an adjuvant.

Methods of inducing an immune response to filovirus GP in a subject are disclosed. In such methods a subject, such as a human subject, is administered an effective amount of a disclosed immunogenic composition to elicit the immune response. The subject can be, for example, a human subject at risk of or having an ebolavirus infection.

The foregoing and other features and advantages of this disclosure will become more apparent from the following detailed description of several embodiments which proceeds with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1C. Analysis of antibody repertoires elicited in adults after first and second vaccinations with different doses of rVSVΔG-ZEBOV-GP. (FIG. 1A) Number of captured phage clones isolated using EBOV GFPDL affinity selection with sera from adults after the first and second vaccinations with 3 million, 20 million or 100 million PFU rVSVΔG-ZEBOV-GP vaccine (n=10 per group). (FIGS. 1B and 1C) Schematic alignments of the peptides recognized in sera after the first (FIG. 1B) and second (FIG. 1C) vaccinations, identified by panning with EBOV GFPDL Amino acid designations are based on the GP protein sequence encoded by the complete EBOV GP gene (FIG. 9). SP, signal peptide; HR1, heptad repeat 1; HR2, heptad repeat 2; TM, transmembrane domain; CT, cytoplasmic tail. Bars indicate identified inserts in GP sequence. Graphical distribution of representative clones with a frequency of ≥2 obtained after affinity selection are shown. The horizontal positions and the lengths of the bars indicate the peptide sequence displayed on the selected phage clone to its homologous sequence in the EBOV GP sequence on alignment. The thickness of each bar represents the frequency of repetitively isolated phage, with the scale shown below the alignment. The GFPDL affinity selection was performed in quadruplicate (two independent experiments by two different investigators, who were blinded to sample identity).

FIGS. 2A-2C. Elucidation of antibody epitope profile against Ebola GP after rVSVΔG-ZEBOV-GP vaccination in humans. (FIG. 2A) Antigenic sites within the EBOV GP recognized by serum antibodies after vaccination (based on data presented in FIG. 1) Amino acid designations are based on the GP protein sequence encoded by the complete EBOV GP gene (FIG. 9). Epitopes previously described using MAbs are shown above the GP schematic. Critical residues for binding of MAbs in anti-EBOV cocktails ZMAb (1H3 (blue asterisks) and 2G4 and 4G7 (pink asterisks)), MB-003 (13C6 (red asterisks), 6D8 and 13F6) and MAb KZ52 (Davidson, E. et al. J. Virol. 89, 10982-10992, 2015) are shown. (FIGS. 2B and 2C) Distribution and frequency of phage clones expressing each of the key GP antigenic sites after first (FIG. 2B) or second (FIG. 2C) vaccination across dosage groups (3 million PFU, 20 million PFU and 100 million PFU). The number of clones encoding each antigenic site was divided by the total number of EBOV GFPDL-selected clones for pooled sera from each vaccine-dose group and represented as a percentage. Error bars represent s.e.m. of 4 independent experiments. The GFPDL affinity selection was performed in quadruplicate.

FIG. 3A-3B. Structural representation of antigenic sites in EBOV GP identified with GFPDL. Representations of individual antigenic sites on the surface structures of a complete EBOV GP model (left) and solved EBOV GP structure (PDB 3CSY) (Lee, J. E. et al. Nature 454, 177-182, 2008) are shown (right) where available; antigenic sites in a monomer (chain A) are color coded as in FIG. 2. The EBOV GP structure used for crystallography encompasses amino acid residues 33-189, 214-278, 299-310 and 502-599 of the mature 676-aa GP sequence. The transmembrane (TM) domain is shown in orange, and the viral membrane is shown (gray bar) on the model images. Sites I, II and VI on the model are shown in front view. Sites II.1, II.2, III, III.1, IV, IV.1, IV.2, IV.3, V and V.1-V.7 are shown in rear view. All sites (except site I) are depicted in front view on the solved structure.

FIGS. 4A-4F. SPR-based analysis of sera from rVSVΔG-ZEBOV-GP-vaccinated individuals with EBOV GP purified protein. (FIGS. 4A and 4B) Total binding (RU) to purified mature GP from Mayinga (FIG. 4A) or Makona (FIG. 4B) EBOV strains in serum samples collected at different time points from adults receiving vaccine or placebo intramuscularly on day 0 (DO) and day 28 (D28). Maximum RU values for GP binding by serum antibodies obtained from all individuals are shown. Data are mean±s.d. No significant differences were found between groups (P≥0.05, multiple-comparison adjustment using Bonferroni method). (FIG. 4C) EBOV neutralization endpoint titers of serum antibodies in pseudovirus neutralization assay (PsVNA) used for EBOV GFPDL-based epitope mapping. PsVNA80 titer refers to the highest serum dilutions required to achieve 80% viral inhibition. (FIG. 4D) Correlation between maximum RU for post-vaccination sera against Makona GP and homologous virus neutralization titers (PsVNA80; Spearman r=0.7598, P≤0.0001) after the first (day 28) and second (day 56) vaccinations. (FIG. 4E) Polyclonal antibody affinity to EBOV GP after rVSVΔG-ZEBOV-GP vaccination. SPR analysis of post-vaccination sera was performed with Makona GP to determine the Kd of polyclonal serum antibodies from all individuals at different post-vaccination time points. Horizontal bars indicate mean values. *P<0.05; **P<0.01; ***P<0.001. (FIG. 4F) Correlation of GP-binding affinity, as measured by Kd of post-vaccination human polyclonal antibodies against Makona GP, with the homologous virus neutralization titers (PsVNA80; Spearman r=0.876, P<0.0001) after the first (day 28) and second (day 56) vaccinations. All SPR experiments were performed twice.

FIGS. 5A-5F. Antibody isotypes in human serum binding to EBOV GP after vaccination and the role of IgM antibodies in virus neutralization. (FIG. 5A) Isotypes of serum antibodies bound to EBOV GP for samples collected from adults from each of the three vaccine-dose groups at different time points, as measured in SPR. RU values for each anti-GP antibody isotype were divided by the total combined RU value for all isotypes for individual serum samples and represented as a percentage. (FIG. 5B) GP binding of IgG and IgM fractions purified from day 28 (VSV-rGP-D28) sera of one of the three subjects with equivalent representations of IgG and IgM isotypes in the EBOV GP-bound antibodies. (FIGS. 5C and 5D) Confirmation of the purity of isotype binding to GP using antihuman IgG (FIG. 5C) and anti-human IgM (FIG. 5D) secondary antibodies. (FIGS. 5E and 5F) Pseudovirus neutralization assay to evaluate purified IgG and IgM antibodies for virus neutralization against Kikwit (FIG. 5E) and Makona (FIG. 5F) EBOV strains. The data are represented as the relative contributions of IgM and IgG antibodies to the total neutralization observed for each sample. Error bars represent mean±s.e.m. of 2 technical replicates. All SPR experiments were replicated twice.

FIGS. 6A and 6B. Antigenic regions/sites of Zaire ebolavirus GP set forth as SEQ ID NO: 35 identified using GFPDL. The residues of SEQ ID NO: 35 for each sequence are indicated in the table. Table showing frequency of antigenic sites for different vaccine dose groups after first and second rVSVΔG-ZEBOV-GP vaccination. The frequency of the clone per antigenic site is calculated by dividing the frequency of occurrence of a particular clone by the total number of phage clones for each vaccine dose.

FIG. 7. Sequence conservation of antigenic regions/sites among different strains and species of ebolavirus. The reference sequence used for determining sequence conservation was SEQ ID NO: 35, and the residue numbering shown in the figure corresponds to SEQ ID NO: 35. Antigenic sites in the GP that are >70% conserved in diverse EBOV strains are shown in bold.

FIG. 8. Phage Titers from affinity selection of pooled sera with different doses of rVSVΔG-ZEBOV-GP vaccine following first vaccination using Protein A/G, IgM and IgA matrices.

FIG. 9. Complete Zaire ebolavirus Mayinga (1976) GP gene translated sequence (SEQ ID NO: 35) used for construction of Zaire ebolavirus-GFPD library and depiction in FIGS. 1-3.

FIGS. 10A and 10B. Alignment of glycoprotein (GP) sequences from Zaire ebolavirus Mayinga (1976, SEQ ID NO: 35), Kikwit (1995, SEQ ID NO: 36) and Makona (2014, SEQ ID NO: 37) strains.

FIG. 11. Random distribution of size and sequence of the EBOV-GFPDL. Sequencing of GP fragments expressed by the phages of the EBOV GFPD libraries were aligned to the Zaire EBOV GP translated sequence (shown in FIG. 9).

FIG. 12. GFPDL based epitope mapping of protective MAbs 6D8 and 13F6 used in the MB-003 cocktail. Graphical distribution of representative clones with a frequency of >2, obtained after affinity selection, are shown. The common conserved minimal sequence (residues of SEQ ID NO: 35, residue numbering is shown in the figure) for each Mab identified using GFPDL mapping is shown in the table compared to the sequence previously identified ‘known site’ (Davidson, E. et al. J. Virol. 89, 10982-10992, 2015). The reactivity of the GFPDL identified sequence to the respective MAb was confirmed by phage ELISA.

FIGS. 13A-13C. GFPDL based epitope mapping of cross-reactive conformation dependent neutralizing and protective human MAb 289 and MAb 324 from EBOV survivors (Flyak, A. I. et al. Cell 164, 392-405, 2016). The reactivity of the GFPDL identified sequence to the respective MAb was confirmed by phage ELISA shown in FIGS. 13B and 13C using the indicated phage clones.

FIG. 14. Anti-GP reactivity of post-second vaccination sera for 20 million and 100 million pfu vaccine dose in ELISA before and after EBOVGFPDL adsorption. Post second vaccination sera from individuals vaccinated with 20 million and 100 million rVSVΔG-ZEBOV-GP vaccine dose was adsorbed on EBOV GFPDL coated petri dishes. Binding to recombinant EBOV-GP is shown before and after GFPDL-adsorption (the after condition is indicated by “M13 ads”) in ELISA using HRP conjugated goat anti-human IgA⁺ IgG⁺ IgM specific antibody.

FIG. 15. Model of the complete Zaire Ebola GP monomer generated using I-TASSER (left) showing transmembrane (TM) domain and membrane, and solved crystal GP structure (PDB Id #3CSY; includes GP residues 33-189, 214-278, 299-310 and 502-599) in monomeric form on right.

FIGS. 16A-16C. Anti-GP reactivity of post-first and post-second vaccination sera for 20 million and 100 million pfu vaccine dose in ELISA. The isotype of two-fold serial dilution of serum antibodies (starting at 200-fold serum dilution) bound to EBOV-GP are shown for serum samples collected at different time points from adults vaccinated with 20 million and 100 million rVSVΔG-ZEBOV-GP vaccine dose administered groups as measured in ELISA using HRP conjugated anti-human IgM muchain specific antibody (FIG. 16A), HRP conjugated anti-human IgG Fc-chain specific antibody (FIG. 16B) and HRP conjugated anti-human IgA alpha-chain specific antibody (FIG. 16C).

FIG. 17. IgG subclass of human serum binding to EBOV-GP following rVSVΔG-ZEBOV-GP vaccination. The subclass of total IgG of serum antibodies bound to EBOV-GP are shown for serum samples collected at different time points from adults vaccinated with three different rVSVΔG-ZEBOV-GP vaccine dose administered groups as measured in SPR experiment. The resonance unit for each anti-GP antibody IgG subclass was divided by the total resonance units for total bound IgG antibodies combined for each sera and represented as a percentage.

FIGS. 18A-18C. Individual antibody repertoires elicited following first vaccination with rVSVΔG-ZEBOV-GP vaccine using IgA, IgG and IgM specific capture beads. (FIG. 18A) Number of captured phage clones isolated using EBOV-GFPDL affinity selection with sera obtained from individual vaccinee after first vaccination with 20 or 100 million pfu rVSVΔGZEBOV-GP vaccine dose group using IgA, IgG and IgM specific capture beads by EBOVKikwit GP GFPDL. (FIG. 18B, FIG. 18C) Schematic alignment of the peptides recognized by IgG, IgM and IgA antibodies following first vaccination with 20 million (FIG. 18B) and 100 million (FIG. 18C) rVSVΔGZEBOV-GP vaccine, identified by panning with GFPDL. The amino acid designation is based on the GP protein sequence encoded by the complete EBOV GP gene (FIGS. 10A and 10B). Bars indicate identified inserts in GP sequence. The GP receptor binding region (RBR) and the mucin like domain are indicated. Bars indicate identified inserts in GP sequence. Bar location indicates the homology of the displayed EBOV-GP protein sequence on the phage clones after affinity selection. Graphical distribution of representative clone with a frequency of >2, obtained after affinity selection, are shown. The thickness of each bar represents the frequency of repetitively isolated phage, with the scale shown below the alignment.

FIGS. 19A-19C. Sequence alignment of GP proteins from Zaire ebolavirus Mayinga (SEQ ID NO: 35), Zaire ebolavirus Kikwit (SEQ ID NO: 36), Zaire ebolavirus Makona (SEQ ID NO: 37), Bundibugyo ebolavirus (SEQ ID NO: 38), Sudan ebolavirus (SEQ ID NO: 39), Tai Forest ebolavirus (SEQ ID NO: 41), and Marburg marburgvirus (SEQ ID NO: 42)

FIG. 20. Sequence of identified antigenic sites of Zaire ebolavirus Mayinga GP (SEQ ID NO: 35).

FIG. 21. Rabbit immunization of GP antigenic site peptides induces high antibody binding to homologous and heterologous native GP.

FIG. 22. Conserved antigenic sites in GP1 induce neutralizing antibodies.

FIG. 23. Zaire ebolavirus challenge study in mice Immunization with peptides from Antigenic sites V.7 in GP1 and VI in GP2 induces sterilizing immunity, while other sites provide partial protection against Ebola virus.

FIG. 24. Conserved antigenic sites in V.7 in GP1 and VIA in GP2 provide significant protection from weight loss following Zaire ebolavirus challenge, while other sites provide partial protection against Ebola virus.

FIG. 25. Conserved antigenic sites in the C-terminal region of GP1 and GP2 generate strong binding antibodies to both Mayinga and Makona GP as measured by surface plasmon resonance.

FIG. 26. Sera from human Ebola virus survivors shows higher antibody binding to diverse antigenic sites in GP than post-vaccination sera.

FIG. 27. Identification of GP antigenic sites that strongly correlate with Ebola neutralization titers (PsVN).

FIG. 28. Spatial structure of linear neutralizing and protective antigenic sites in GP.

SEQUENCES

The nucleic and amino acid sequences listed herein are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. The Sequence Listing is submitted as an ASCII text file in the form of the file named “Sequence.txt” (˜28 kb), which was created on Jun. 9, 2020 which is incorporated by reference herein.

SEQ ID NOs: 1-34 and 43-61 are the amino acid sequences of immunogenic peptides, as follows:

SEQ ID NO: 1:  TTEDHKIMASENSSAMVQVHSQGREAAVSH SEQ ID NO: 8:  TX₁₀EDHKIMASENSSAMVQVHSQGRX₁₁AAVSH wherein: X₁₀ is T or N; and X₁₁ is E or K. Antigenic site II.1 peptides, residues 152-220: SEQ ID NO: 47:  AFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLR EPVNATEDPSSGYYSTTIRY  (Zaire ebolavirus Mayinga, Kikwit, Makona) SEQ ID NO: 48:  AFHKEGAFFLYDRLASTIIYRSTTFSEGVVAFLILPKTKKDFFQSPPLHEP ANMTTDPSSYYHTVTLNY (Bundibugyo ebolavirus) SEQ ID NO: 49:  AFHKDGAFFLYDRLASTVIYRGVNFAEGVIAFLILAKPKETFLQSPPIRE AVNYTENTSSYYATSYLEY  (Sudan ebolavirus) SEQ ID NO: 50:  AFHKEGAFFLYDRLASTIIYRGTTFAEGVIAFLILPKARKDFFQSPPLHEP ANMTTDPSSYYHTTTINY  (Ta ï  Forest ebolavirus) SEQ ID NO: 61:  ALHLWGAFFLYDRIASTTMYRGKVFTEGNIAAMIVNKTVHKMIFSRQG QGYRHMNLTSTNKYWTSSNGT  (Margburg margburgvirus) Antigenic site IV.1 peptides, residues 282-305: SEQ ID NO: 17:  DTTIGEWAFWETKKNLTRKIRSEE, Zaire ebolavirus Mayinga, Kikwit, Makona) SEQ ID NO: 18:  DTGVGEWAFVVENKKNFTKTLSSEE (Bundibugyo ebolavirus) SEQ ID NO: 19:  NADIGEWAFVVENKKNLSEQLRGEE (Sudan ebolavirus) SEQ ID NO: 20:  DTSMGEWAFVVENKKNFKKTLSSEE (Ta ï  Forest ebolavirus) SEQ ID NO: 58:  DEDLATSGSGSGEREPHTTSD (Margburg margburgvirus) Antigenic site IV.2 peptides, residues 286-296: SEQ ID NO: 51:  GEWAFVVETKKN (Zaire ebolavirus Mayinga, Kikwit, Makona); SEQ ID NO: 52:  GEWAFVVENKKN (Bundibugyo ebolavirus, Sudan ebolavirus, Ta ï  Forest ebolavirus); SEQ ID NO: 62:  ATSGSGSGER  (Margburg margburgvirus) Antigenic site  V.1 peptides, residues 343-368: SEQ ID NO: 21:  ASENSSAMVQVHSQGREAAVSHLTTL (Zaire ebolavirus Mayinga, Kikwit) SEQ ID NO: 22:  ASENSSAMVQVHSQGRKAAVSHLTTL (Zaire ebolavirus Makona) SEQ ID NO: 23:  VPKDPASVVQVRDLQRENTVPTSP (Bundibugyo ebolavirus) SEQ ID NO: 24:  VPKNSPGVVPLHIPEGETTLPSQNST (Sudan ebolavirus) SEQ ID NO: 25:  VSEDSTPVVQMQNIKGKDTMPTTV (Ta ï  Forest ebolavirus) SEQ ID NO: 59:  LDKNNTTAQPSMPPHNTTTISTNNTS (Margburg margburgvirus) Antigenic site V.6 peptides, residues 457-484 and 546-484: SEQ ID NO: 2:  ETAGNNNTHHQDTGEESASSGKLGLITN (Zaire ebolavirus Mayinga, Kikwit, Makona) SEQ ID NO: 26:  MITSHDTDSNRPNPIDISESTEPGLLTN (Bundibugyo ebolavirus) SEQ ID NO: 27:  LTTPENITTAVKTVLPQESTSNGLITS (Sudan ebolavirus) SEQ ID NO: 28:  LPEQHTAASAIPRAVHPDELSGPGFLTN (Ta ï  Forest ebolavirus) SEQ ID NO: 56:  LWREGDMFPFLDGLINAPIDFDPVPTK (Margburg margburgvirus) SEQ ID NO: 43:  SETAGNNNTHHQDTGEESASSGKLGLITN (Zaire ebolavirus Mayinga, Kikwit, Makona) SEQ ID NO: 44:  TMITSHDTDSNRPNPIDISESTEPGLLTN (Bundibugyo ebolavirus) SEQ ID NO: 45:  TLTTPENITTAVKTVLPQESTSNGLITS (Sudan ebolavirus) SEQ ID NO: 46:  TLPEQHTAASAIPRAVHPDELSGPGFLTN (Ta ï  Forest ebolavirus) SEQ ID NO: 57:  ILWREGDMFPFLDGLINAPIDFDPVPTK (Margburg margburgvirus) Antigenic site V.7 peptides, residues 469-498: SEQ ID NO: 3:  TGEESASSGKLGLITNTIAGVAGLITGGRR (Zaire ebolavirus Mayinga, Kikwit, Makona) SEQ ID NO: 32:  NPIDISESTEPGLLTNTIRGVANLLTGSRR (Bundibugyo ebolavirus) SEQ ID NO: 33:  TVLPQESTSNGLITSTVTGILGSLGLRKR (Sudan ebolavirus) SEQ ID NO: 34:  RAVHPDELSGPGFLTNTIRGVTNLLTGSRR (Ta ï  forest ebolavirus) SEQ ID NO: 55:  GLINAPIDFDPVPNTKTIFDESSSSGASAE (Margburg margburgvirus) Antigenic site V.10 peptides, residues 520-547: SEQ ID NO: 29:  TQDEGAAIGLAWIPYFGPAAEGIYIEGL (Zaire ebolavirus Mayinga) SEQ ID NO: 30:  TQDEGAAIGLAWIPYFGPAAEGIYTEGL (Zaire ebolavirus Kikwit, Makona, Sudan ebolavirus) SEQ ID NO: 31:  TQDEGAAIGLAWIPYFGPAAEGIYTEGI (Bundibugyo ebolavirus, Ta ï  Forest ebolavirus) SEQ ID NO: 60:  VQEDDLAAGLSWIPFFGPGIEGLYTAGL (Margburg margburgvirus) Antigenic site VI peptides, residues 617-645 or 617-646: SEQ ID NO: 9  (KNITDKIX₁QIIHDFX₂DX₃X₄TLPX₅QX₆X₇X₈X₉NWW, wherein X₁ is D or N, X₂ is V or I, X₃ is K or N, X₄ is T, P, or N, X₅ is D or  N, X₆ is G, T, D, or N, X₇ is D or N, X₈ is N, D, or G, and X₉ is D or S (Antigenic site VI consensus,) SEQ ID NO: 10:  KNITDKIDQIIHDFVDKTLPDQGDNDNWW (Zaire ebolavirus Mayinga, Kikwit, Makona) SEQ ID NO: 11:  KNITDKINQIIHDFIDKPLPDQTDNDNWW (Bundibugyo ebolavirus) SEQ ID NO: 12:  KNITDKIDQIIHDFIDNPLPNQDNDDNWW (Sudan ebolavirus) SEQ ID NO: 13:  KNITDKINQIIHDFVDNNLPNQNDGSNWW (Ta ï  Forest ebolavirus) SEQ ID NO: 53: KNISEQIDQIKKDEQKEGTGWGLGGKWW (Margburg margburgvirus) SEQ ID NO: 7:  KNITDKIX₁QIIHDFX₂DX₃X₄TLPX₅QX₆X₇X₈X₉NWWT, wherein: X₁ is D or N, X₂ is V and I, X₃ is K or N, X₄ is T, P, or  N, X₅ is D or N, X₆ is G, T, D, or N, X₇ is D or N, X₈ is N, D, or G; and X₉ is D or S SEQ ID NO: 4:  KNITDKIDQIIHDFVDKTLPDQGDNDNWWT (Zaire ebolavirus Mayinga, Kikwit, Makona) SEQ ID NO: 14:  KNITDKINQIIHDFIDKPLPDQTDNDNWWT (Bundibugyo ebolavirus) SEQ ID NO: 15:   KNITDKIDQIIHDFIDNPLPNQDNDDNWWT  (Sudan ebolavirus) SEQ ID NO: 16:  KNITDKINQIIHDFVDNNLPNQNDGSNWWT  (Ta ï  Forest ebolavirus) SEQ ID NO: 54:  KNISEQIDQIKKDEQKEGTGWGLGGKWWT  (Margburg margburgvirus) Antigenic site VI.1 peptides, residues 630-646: SEQ ID NO: 6  (FX₂DX₃X₄TLPX₅QX₆X₇X₈X₉NWWT, wherein: X₂ is selected from V and I; X₃ from K and N; X₄ from T, P, and N; X₅ and X₇ from D and N; X₆ from G, T, D, and N; X₈ from N, D, and G; and X₉ from D and S SEQ ID NO: 5:  FVDKTLPDQGDNDNWWT  (Zaire ebolavirus Mayinga, Kikwit, Makona) Residues 14-30 of SEQ ID NO: 14:  KNITDKINQIIHDFIDKPLPDQTDNDNWWT (Bundibugyo ebolavirus) Residues 14-30 of SEQ ID NO: 15:  KNITDKIDQIIHDFIDNPLPNQDNDDNWWT  (Sudan ebolavirus) Residues 14-30 of SEQ ID NO: 16:  KNITDKINQIIHDFVDNNLPNQNDGSNVVWT  (Ta ï  Forest ebolavirus) SEQ ID NO: 35 is an exemplary amino acid sequence of a precursor of the GP from the Mayinga Strain of Zaire ebolavirus (GENBANK Acc. No. AIO11753.1, which is incorporated by reference herein in its entirety). MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVAT DVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFH KEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETE YLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSF TVVSNGAKNISGQSPARTSSDPGTNTTTEDHKIMASENSSAMVQVHSQGREAAVSHLTTLATISTSPQSLTTKPGPD NSTHNTPVYKLDISEATQVEQHHRRTDNDSTASDTPSATTAAGPPKAENTNTSKSTDFLDPATTTSPQNHSETAGNN NTHHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRREAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAA EGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWT KNITDKIDQIIHDFVDKTLPDQGDNDNWWTGWRQWIPAGIGVTGVIIAVIALFCICKFVF SEQ ID NO: 36 is an exemplary amino acid sequence of a precursor of the GP from the Kikwit Strain of Zaire ebolavirus (GENBANK Acc. No. AIO11753.1, which is incorporated by reference herein in its entirety). MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVAT DVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFH KEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETE YLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSF TAVSNRAKNISGQSPARTSSDPGTNTTTEDHKIMASENSSAMVQVHSQGREAAVSHLTTLATISTSPQPPTTKPGPD NSTHNTPVYKLDISEATQVEQHHRRTDNDSTASDTPPATTAAGPLKAENTNTSKGTDLLDPATTTSPQNHSETAGNN NTHHQDTGEESASSGKLGLITNTIAGVAGLITGGRRARREAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAA EGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWT KNITDKIDQIIHDFVDKTLPDQGDNDNWWTGWRQWIPAGIGVTGVIIAVIALFCICKFVF SEQ ID NO: 37 is an exemplary amino acid sequence of a precursor of the GP from the Makona Strain of Zaire ebolavirus (GENBANK Acc. No. AIO11753.1, which is incorporated by reference herein in its entirety). MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSTNQLRSVGLNLEGNGVATSIPLGVIHNSTLQVSDVDKLVCRDKLS DVPSVTKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFH KEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSGYYSTTIRYQATGFGTNETESHPLREPVNATEDPS YLFEVDNLTYVQLESRFTPQFLLQLNETIYASGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSF TAVSNGPKNISGQSPARTSSDPETNTTNEDHKIMASENSSAMVQVHSQGRKAAVSHLTTLATISTSPQPPTTKTGPD NSTHNTPVYKLDISEATQVGQHHRRADNDSTASDTPPATTAAGPLKAENTNTSKSADSLDLATTTSPQNYSETAGNN NTHHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRREVIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAA EGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWT KNI TDKI DQII HDFVDKTLPDQGDNDNWWTGWRQWIPAGIGVTGVIIAVIALFCICKFVF SEQ ID NO: 38 is an exemplary amino acid sequence of a precursor of the GP from Bundibugyo ebolavirus (GENBANK Acc. No. AGL73460.1, which is incorporated by reference herein in its entirety). MVTSGILQLPRERFRKTSFFVWVIILFHKVFPIPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLKSVGLNLEGNGVAT DVPTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTGPCPEGFAFH KEGAFFLYDRLASTIIYRSTTFSEGVVAFLILPKTKKDFFQSPPLHEPANMTTDPSSYYHTVTLNYVADNFGTNMTN FLFQVDHLTYVQLEPRFTPQFLVQLNETIYTNGRRSNTTGTLIWKVNPTVDTGVGEWAFWENKKNFTKTLSSEELSV ILVPRAQDPGSNQKTKVTPTSFANNQTSKNHEDLVPKDPASVVQVRDLQRENTVPTSPLNTVPTTLIPDTMEEQTTS HYELPNISGNHQERNNTAHPETLANNPPDNTTPSTPPQDGERTSSHTTPSPRPVPTSTIHPTTRETQIPTTMITSHD TDSNRPNPIDISESTEPGLLTNTIRGVANLLTGSRRTRREITLRTQAKCNPNLHYWTTQDEGAAIGLAWIPYFGPAA EGIYTEGIMHNQNGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWT KNITDKIDQIIHDFIDKPLPDQTDNDNWWTGWRQWVPAGIGITGVIIAVIALLCICKFLL SEQ ID NO: 39 is an exemplary amino acid sequence of a precursor of the GP from Sudan ebolavirus (GENBANK Acc. No. ACR33190.1, which is incorporated by reference herein in its entirety). MEGLSLLQLPRDKFRKSSFFVWVIILFQKAFSMPLGVVTNSTLEVTEIDQLVCKDHLASTDQLKSVGLNLEGSGVST DIPSATKRWGFRSGVPPKVFSYEAGEWAENCYNLEIKKPDGSECLPPPPDGVRGFPRCRYVHKAQGTGPCPGDYAFH KDGAFFLYDRLASTVIYRGVNFAEGVIAFLILAKPKETFLQSPPIREAVNYTENTSSYYATSYLEYEIENFGAQHST TLFKINNNTFVLLDRPHTPQFLFQLNDTIHLHQQLSNTTGKLIWTLSEQLRGEELSFDANINADIGEWAFWENKKNL ETLSLNETEDDDATSSRTTKGRISDRATRKYSDLVPKDSPGMVSLHVPEGETTLPSQNSTEGRRVDVNTQETITETT ATIIGTNGNNMQISTIGTGLSSSQILSSSPTMAPSPETQTSTTYTPKLPVMTTEESTTPPRNSPGSTTEAPTLTTPE NITTAVKTVLPQESTSNGLITSTVTGILGSLGLRKRSRRQVNTRATGKCNPNLHYWTAQEQHNAAGIAWIPYFGPGA EGIYTEGLMHNQNALVCGLRQLANETTQALQLFLRATTELRTYTILNRKAIDFLLRRWGGTCRILGPDCCIEPHDWT KNITDKINQIIHDFIDNPLPNQDNDDNWWTGWRQWIPAGIGITGIIIAIIALLCVCKLLC SEQ ID NO: 40 is an exemplary amino acid sequence of a precursor of the GP from Reston ebolavirus (GENBANK Acc. No. AAC54891.1, which is incorporated by reference herein in its entirety). MGSGYQLLQLPRERFRKTSFLVWVIILFQRAISMPLGIVTNSTLKATEIDQLVCRDKLSSTSQLKSVGLNLEGNGIA TDVPSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKSDGSECLPLPPDGVRGFPRCRYVHKVQGTGPCPGDLAF HKNGAFFLYDRLASTVIYRGTTFTEGVVAFLILSEPKKHFWKATPAHEPVNTTDDSTSYYMTLTLSYEMSNFGGKES NTLFKVDNHTYVQLDRPHTPQFLVQLNETLRRNNRLSNSTGRLTWTLDPKIEPDVGEWAFWETKKNFSQQLHGENLH FQILSTHTNNSSDQSPAGTVQGKISYHPPTNNSELVPTDSPPVVSVLTAGRTEEMSTQGLTNGETITGFTANPMTTT IAPSPTMTSEVDNNVPSEQPNNTASIEDSPPSASNETIDHSEMNPIQGSNNSAQSPQTKTTPAPTASPMTQDPQETA NSSKLGTSPGSAAEPSQPGFTINTVSKVADSLSPTRKQKRSVRQNTANKCNPDLHYWTAVDEGAAVGLAWIPYFGPA AEGIYIEGVMHNQNGLICGLRQLANETTQALQLFLRATTELRTYSLLNRKAIDFLLQRWGGTCRILGPSCCIEPHDW TKNITDEINQIKHDFIDNPLPDHGDDLNLWTGWRQWIPAGIGIIGVIIAIIALLCICKILC SEQ ID NO: 41 is an exemplary amino acid sequence of a precursor of the GP from Ta ï  Forest ebolavirus (GENBANK Acc. No. ACI28632.1, which is incorporated by reference herein in its entirety). MGASGILQLPRERFRKTSFFVWVIILFHKVFSIPLGVVHNNTLQVSDIDKFVCRDKLSSTSQLKSVGLNLEGNGVAT DVPTATKRWGFRAGVPPKVVNCEAGEWAENCYNLAIKKVDGSECLPEAPEGVRDFPRCRYVHKVSGTGPCPGGLAFH KEGAFFLYDRLASTIIYRGTTFAEGVIAFLILPKARKDFFQSPPLHEPANMTTDPSSYYHTTTINYVVDNFGTNTTE FLFQVDHLTYVQLEARFTPQFLVLLNETIYSDNRRSNTTGKLIWKINPTVDTSMGEWAFWENKKNFTKTLSSEELSF VPVPETQNQVLDTTATVSPPISAHNHAAEDHKELVSEDSTPVVQMQNIKGKDTMPTTVTGVPTTTPSPFPINARNTD HTKSFIGLEGPQEDHSTTQPAKTTSQPTNSTESTTLNPTSEPSSRGTGPSSPTVPNTTESHAELGKTTPTTLPEQHT AASAIPRAVHPDELSGPGFLTNTIRGVTNLLTGSRRKRRDVTPNTQPKCNPNLHYWTALDEGAAIGLAWIPYFGPAA EGIYTEGIMENQNGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPQDWT KNITDKIDQIIHDFVDNNLPNQNDGSNWWTGWKQWVPAGIGITGVIIAIIALLCICKFML SEQ ID NO: 42 is an exemplary amino acid sequence of a precursor of the GP from Marburg margburgvirus (GENBANK Acc. No. AAR85456.1, which is incorporated by reference herein in its entirety). MKTTCFLISLILIQGTKNLPILEIASNNQPQNVDSVCSGTLQKTEDVHLMGFTLSGQKVADSPLEASKRWAFRTGVP PKNVEYTEGEEAKTCYNISVTDPSGKSLLLDPPTNIRDYPKCKTIHHIQGQNPHAQGIALHLWGAFFLYDRIASTTM YRGKVFTEGNIAAMIVNKTVHKMIFSRQGQGYRHMNLTSTNKYWTSSNGTQTNDTGCFGALQEYNSTKNQTCAPSKI PPPLPTARPEIKLTSTPTDATKLNTTDPSSDOEDLATSGSGSGEREPHTTSDAVTKQGLSSTMPPTPSPQPSTPQQG GNNTNHSQDAVTELDKNNTTAQPSMPPHNTTTISTNNTSKHNFSTLSAPLQNTTNDNTQSTITENEQTSAPSITTLP PTGNPTTAKSTSSKKGPATTAPNTTNEHFTSPPPTPSSTAQHLVYFRRKRSILWREGDMFPFLDGLINAPIDFDPVP NTKTIFDESSSSGASAEEDQHASPNISLTLSYFPNINENTAYSGENENDCDAELRIWSVQEDDLAAGLSWIPFFGPG IEGLYTAGLIKNQNNLVCRLRRLANQTAKSLELLLRVTTEERTFSLINRHAIDFLLTRWGGTCKVLGPDCCIGIEDL SKNISEQIDQIKKDEQKEGTGWGLGGKWWTSDWGVLTNLGILLLLSIAVLIALSCICRIFTKYIG

DETAILED DESCRIPTION I. Summary of Terms

Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes X, published by Jones & Bartlett Publishers, 2009; and Meyers et al. (eds.), The Encyclopedia of Cell Biology and Molecular Medicine, published by Wiley-VCH in 16 volumes, 2008; and other similar references.

As used herein, the singular forms “a,” “an,” and “the,” refer to both the singular as well as plural, unless the context clearly indicates otherwise. For example, the term “an antigen” includes single or plural antigens and can be considered equivalent to the phrase “at least one antigen.” As used herein, the term “comprises” means “includes.” It is further to be understood that any and all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for descriptive purposes, unless otherwise indicated. Although many methods and materials similar or equivalent to those described herein can be used, particular suitable methods and materials are described herein. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. To facilitate review of the various embodiments, the following explanations of terms are provided:

Adjuvant: A vehicle used to enhance antigenicity. In some embodiments, an adjuvant can include a suspension of minerals (alum, aluminum hydroxide, or phosphate) on which antigen is adsorbed; or water-in-oil emulsion, for example, in which antigen solution is emulsified in mineral oil (Freund incomplete adjuvant), sometimes with the inclusion of killed mycobacteria (Freund's complete adjuvant) to further enhance antigenicity (inhibits degradation of antigen and/or causes influx of macrophages). In some embodiments, the adjuvant used in a disclosed immunogenic composition is a combination of lecithin and carbomer homopolymer (such as the ADJUPLEX™ adjuvant available from Advanced BioAdjuvants, LLC, see also Wegmann, Clin Vaccine Immunol, 22(9): 1004-1012, 2015). Additional adjuvants for use in the disclosed immunogenic compositions include the QS21 purified plant extract, Matrix M, AS like adjuvants including AS01, MF59, ALFQ or other oil in water or water in oil adjuvants Immunostimulatory oligonucleotides (such as those including a CpG motif) can also be used as adjuvants. Adjuvants include biological molecules (a “biological adjuvant”), such as costimulatory molecules. Exemplary adjuvants include IL-2, RANTES, GM-CSF, TNF-α, IFN-γ, G-CSF, LFA-3, CD72, B7-1, B7-2, OX-40L, 4-1BBL and toll-like receptor (TLR) agonists, such as TLR-9 agonists. Additional description of adjuvants can be found, for example, in Singh (ed.) Vaccine Adjuvants and Delivery Systems. Wiley-Interscience, 2007). Adjuvants can be used in combination with the disclosed immunogens.

Administration: The introduction of a composition into a subject by a chosen route. Administration can be local or systemic. For example, if the chosen route is intravenous, the composition (such as a composition including a disclosed immunogen) is administered by introducing the composition into a vein of the subject. Exemplary routes of administration include, but are not limited to, oral, injection (such as subcutaneous, intramuscular, intradermal, intraperitoneal, and intravenous), sublingual, rectal, transdermal (for example, topical), intranasal, vaginal, and inhalation routes.

Antibody: An immunoglobulin, antigen-binding fragment, or derivative thereof, that specifically binds and recognizes an analyte (antigen), such as a peptide from ebolavirus GP. The term “antibody” is used herein in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments, so long as they exhibit the desired antigen-binding activity. Non-limiting examples of antibodies include, for example, intact immunoglobulins and variants and fragments thereof that retain binding affinity for the antigen. Examples of antibody fragments include but are not limited to Fv, Fab, Fab′, Fab′-SH, F(ab′)₂; diabodies; linear antibodies; single-chain antibody molecules (e.g. scFv); and multispecific antibodies formed from antibody fragments. Antibody fragments include antigen binding fragments either produced by the modification of whole antibodies or those synthesized de novo using recombinant DNA methodologies (see, e.g., Kontermann and Dubel (Ed), Antibody Engineering, Vols. 1-2, 2^(nd) Ed., Springer Press, 2010). Light and heavy chain variable regions contain a “framework” region interrupted by three hypervariable regions, also called “complementarity-determining regions” or “CDRs” (see, e.g., Kabat et al., Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991). The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three-dimensional space. The CDRs are primarily responsible for binding to an epitope of an antigen.

Carrier: An immunogenic molecule to which a peptide can be linked to enhance an immune response to the peptide. Carriers are chosen to increase the immunogenicity of the antigen and/or to elicit antibodies against the carrier which are diagnostically, analytically, and/or therapeutically beneficial. Useful carriers include polymeric carriers, which can be natural (for example, proteins from bacteria or viruses), semi-synthetic or synthetic materials containing one or more functional groups to which a reactant moiety can be attached.

Conjugate: A complex of at least two heterologous molecules linked together. In a non-limiting example, an ebolavirus peptide as disclosed herein is conjugated to a protein carrier by a linker.

Consists essentially of and Consists Of: A polypeptide comprising an amino acid sequence that consists essentially of a specified amino acid sequence does not include any additional amino acid residues. However, the residues in the polypeptide can be modified to include non-peptide components, such as labels (for example, fluorescent, radioactive, or solid particle labels), sugars or lipids, and the N- or C-terminus of the polypeptide can be joined (for example, by peptide bond) to heterologous amino acids, such as a cysteine (or other) residue in the context of a linker for conjugation chemistry. A polypeptide that consists of a specified amino acid sequence does not include any additional amino acid residues, nor does it include additional biological components, such as nucleic acids lipids, sugars, nor does it include labels. However, the N- or C-terminus of the polypeptide can be joined (for example, by peptide bond) to heterologous amino acids, such as a peptide tag, or a cysteine (or other) residue in the context of a linker for conjugation chemistry.

A polypeptide that consists or consists essentially of a specified amino acid sequence can be glycosylated or have an amide modification. A polypeptide that consists of or consists essentially of a particular amino acid sequence can be linked via its N- or C-terminus to a heterologous polypeptide, such as in the case of a fusion protein containing a first polypeptide consisting or a first sequence that is linked (via peptide bond) to a heterologous polypeptide consisting of a second sequence. In another example, the N- or C-terminus of a polypeptide that consists of or consists essentially of a particular amino acid sequence can be linked to a peptide linker (via peptide bond) that is further linked to one or more additional heterologous polypeptides. In a further example, the N- or C-terminus of a polypeptide that consists of or consists essentially of a particular amino acid sequence can be linked to one or more amino acid residues that facilitate further modification or manipulation of the polypeptide.

Control: A reference standard. In some embodiments, the control is a negative control, such as sample obtained from a healthy patient not infected with EBOV. In other embodiments, the control is a positive control, such as a tissue sample obtained from a patient diagnosed with EBOV infection. In still other embodiments, the control is a historical control or standard reference value or range of values (such as a previously tested control sample, such as a group of EBOV patients with known prognosis or outcome, or group of samples that represent baseline or normal values).

A difference between a test sample and a control can be an increase or conversely a decrease. The difference can be a qualitative difference or a quantitative difference, for example a statistically significant difference. In some examples, a difference is an increase or decrease, relative to a control, of at least about 5%, such as at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 150%, at least about 200%, at least about 250%, at least about 300%, at least about 350%, at least about 400%, or at least about 500%.

Ebolavirus: A genus of enveloped, non-segmented, negative-sense, single-stranded RNA viruses that cause ebolavirus disease (EVD), formerly known as Ebola hemorrhagic fever (EHF), in humans. Ebolaviruses spread through human-to-human transmission, with infection resulting from direct contact with blood, secretions, organs or other bodily fluids of infected people, and indirect contact with environments contaminated by such fluids. These may include other Filoviruses.

The symptoms of ebolavirus infection and EVD are well-known. Briefly, in humans, ebolavirus has an initial incubation period of 2 to 21 days (7 days on average, depending on the species) followed by a rapid onset of non-specific symptoms such as fever, extreme fatigue, gastrointestinal complaints, abdominal pain, anorexia, headache, myalgias and/or arthralgias. These initial symptoms last for about 2 to 7 days after which more severe symptoms related to hemorrhagic fever occur, including hemorrhagic rash, epistaxis, mucosal bleeding, hematuria, hemoptysis, hematemesis, melena, conjunctival hemorrhage, tachypnea, confusion, somnolence, and hearing loss. In general, the symptoms last for about 7 to 14 days after which recovery may occur. Death can occur 6 to 16 days after the onset of symptoms. People are infectious as long as their blood and secretions contain the virus, which in some instances can be more than 60 days.

Immunoglobulin M (IgM) antibodies to the virus appear 2 to 9 days after infection whereas immunoglobulin G (IgG) antibodies appear approximately 17 to 25 days after infection, which coincides with the recovery phase. In survivors of EVD, both humoral and cellular immunity are detected, however, their relative contribution to protection is unknown.

Five distinct species of Ebolavirus are known, including Bundibugyo ebolavirus, Reston ebolavirus, Sudan ebolavirus, Taï Forest ebolavirus, and Zaire ebolavirus. Bundibugyo ebolavirus, Sudan ebolavirus, and Zaire ebolavirus have been associated with large outbreaks of EVD in Africa and reported case fatality rates of up to 90%. Exemplary amino acid sequences of GP from Bundibugyo ebolavirus, Reston ebolavirus, Sudan ebolavirus, Taï Forest ebolavirus, and Zaire ebolavirus are set forth as SEQ ID NOs: 25-29.

The ebolavirus genome includes about 19 kb, which encode seven structural proteins including NP (a nucleoprotein), VP35 (a polymerase cofactor), VP30 (a transcriptional activator), VP24, L (a RNA polymerase), and GP (a glycoprotein).

Ebolavirus glycoprotein (GP): The virion-associated transmembrane glycoprotein of Ebolavirus is initially synthesized as a precursor protein of about 676 amino acids in size, designated GP₀. Individual GP₀ polypeptides form a homotrimer and undergo glycosylation as well as processing to remove the signal peptide, and cleavage by a cellular protease between approximately positions 501/502 to generate separate GP₁ and GP₂ polypeptide chains, which remain associated via disulfide bonds as GP₁/GP₂ protomers within the homotrimer. The extracellular GP₁ trimer (approx. 140 kDa) is derived from the amino-terminal portion of the GP₀ precursors, and the GP₂ trimer (approx. 26 kDa), which includes extracellular, transmembrane, and cytosolic domains, is derived from the carboxyl-terminal portion of the GP₀ precursors. GP₁ is responsible for attachment to new host cells while GP₂ mediates fusion with those cells.

Comparisons of the predicted amino acid sequences for the GPs of the different ebolaviruses show conservation of amino acids in the amino-terminal and carboxy-terminal regions with a highly variable region in the middle of the protein (Feldmann el al., Virus Res. 24: 1-19, 1992). The GPs of the ebolaviruses are highly glycosylated and contain both N-linked and O-linked carbohydrates that contribute up to 50% of the molecular weight of the protein. Most of the glycosylation sites are found in the central variable region of GP.

The numbering used in the disclosed filovirus GPs and fragments thereof is relative to the Zaire ebolavirus GP protein set forth as SEQ ID NO: 35, unless context indicates otherwise.

Effective amount: An amount of agent, such as an immunogen, that is sufficient to generate a desired response, such as an immune response in a subject. It is understood that to obtain a protective immune response against an antigen of interest can require multiple administrations of a disclosed immunogen, and/or administration of a disclosed immunogen as the “prime” in a prime boost protocol wherein the boost immunogen can be different from the prime immunogen. Accordingly, an effective amount of a disclosed immunogen can be the amount of the immunogen sufficient to elicit a priming immune response in a subject that can be subsequently boosted with the same or a different immunogen to generate a protective immune response.

In one example, a desired response is to induce an immune response that inhibits or prevents Ebola virus infection in a subject. For example, administration of an effective amount of a disclosed ebolavirus GP peptide can induce an immune response in a subject that inhibits subsequent infection of the subject by an ebolavirus.

Expression: Transcription or translation of a nucleic acid sequence. For example, a gene is expressed when its DNA is transcribed into an RNA or RNA fragment, which in some examples is processed to become mRNA. A gene may also be expressed when its mRNA is translated into an amino acid sequence, such as a protein or a protein fragment. In a particular example, a heterologous gene is expressed when it is transcribed into an RNA. In another example, a heterologous gene is expressed when its RNA is translated into an amino acid sequence. The term “expression” is used herein to denote either transcription or translation. Regulation of expression can include controls on transcription, translation, RNA transport and processing, degradation of intermediary molecules such as mRNA, or through activation, inactivation, compartmentalization or degradation of specific protein molecules after they are produced.

Expression control sequences: Nucleic acid sequences that regulate the expression of a heterologous nucleic acid sequence to which it is operatively linked. Expression control sequences are operatively linked to a nucleic acid sequence when the expression control sequences control and regulate the transcription and, as appropriate, translation of the nucleic acid sequence. Thus expression control sequences can include appropriate promoters, enhancers, transcription terminators, a start codon (ATG) in front of a protein-encoding gene, splicing signals for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons. The term “control sequences” is intended to include, at a minimum, components whose presence can influence expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. Expression control sequences can include a promoter.

A promoter is a minimal sequence sufficient to direct transcription. Also included are those promoter elements which are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue-specific, or inducible by external signals or agents; such elements may be located in the 5′ or 3′ regions of the gene. Both constitutive and inducible promoters are included (see for example, Bitter et al., Methods in Enzymology 153:516-544, 1987). For example, when cloning in bacterial systems, inducible promoters such as pL of bacteriophage lambda, plac, ptrp, ptac (ptrp-lac hybrid promoter) and the like may be used. In one embodiment, when cloning in mammalian cell systems, promoters derived from the genome of mammalian cells (such as metallothionein promoter) or from mammalian viruses (such as the retrovirus long terminal repeat; the adenovirus late promoter; the vaccinia virus 7.5K promoter) can be used. Promoters produced by recombinant DNA or synthetic techniques may also be used to provide for transcription of the nucleic acid sequences.

A polynucleotide can be inserted into an expression vector that contains a promoter sequence which facilitates the efficient transcription of the inserted genetic sequence of the host. The expression vector typically contains an origin of replication, a promoter, as well as specific nucleic acid sequences that allow phenotypic selection of the transformed cells.

Expression vector: A vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.

Heterologous: Originating from a different genetic source. A nucleic acid molecule that is heterologous to a cell originated from a genetic source other than the cell in which it is expressed. Methods for introducing a heterologous nucleic acid molecule in a cell or organism include, for example, transformation with a nucleic acid, including electroporation, lipofection, particle gun acceleration, and homologous recombination.

Immune response: A response of a cell of the immune system, such as a B cell, T cell, or monocyte, to a stimulus. In one embodiment, the response is specific for a particular antigen (an “antigen-specific response”). In one embodiment, an immune response is a T cell response, such as a CD4+ response or a CD8+ response. In another embodiment, the response is a B cell response, and results in the production of specific antibodies. “Priming an immune response” refers to treatment of a subject with a “prime” immunogen to induce an immune response that is subsequently “boosted” with a boost immunogen. Together, the prime and boost immunizations produce the desired immune response in the subject. “Enhancing an immune response” refers to co-administration of an adjuvant and an immunogenic agent, wherein the adjuvant increases the desired immune response to the immunogenic agent compared to administration of the immunogenic agent to the subject in the absence of the adjuvant.

Immunogen: A protein or a portion thereof that is capable of inducing an immune response in a mammal, such as a mammal infected or at risk of infection with a pathogen.

Immunogenic composition: A composition comprising a disclosed immunogen, or a nucleic acid molecule or vector encoding a disclosed immunogen, that elicits a measurable CTL response against the immunogen, or elicits a measurable B cell response (such as production of antibodies) against the immunogen, when administered to a subject. It further refers to isolated nucleic acids encoding an immunogen, such as a nucleic acid that can be used to express the immunogen (and thus be used to elicit an immune response against this immunogen). For in vivo use, the immunogenic composition will typically include the protein or nucleic acid molecule in a pharmaceutically acceptable carrier and may also include other agents, such as an adjuvant.

Inhibiting a disease or condition: Reducing the full development of a disease or condition in a subject, for example, reducing the full development of Ebola virus disease in a subject who has an Ebola virus infection, and/or reducing Ebola virus infection in a subject or population of subjects at risk thereof. This includes neutralizing, antagonizing, prohibiting, preventing, restraining, slowing, disrupting, stopping, or reversing progression or severity of the disease or condition.

Inhibiting a disease or condition refers to a prophylactic intervention administered before the disease or condition has begun to develop (for example, by vaccinating a subject at risk of EBOV infection, but not infected by EBOV, with an ebolavirus GP peptide immunogen as disclosed herein) that reduces subsequent development of the disease or condition, and also to amelioration of one or more signs or symptoms of the disease or condition following development. The term “ameliorating,” with reference to inhibiting a disease or condition refers to any observable beneficial effect of the intervention intended to inhibit the disease or condition. The beneficial effect can be evidenced, for example, by a delayed onset of clinical symptoms of the disease or condition in a susceptible subject, a reduction in severity of some or all clinical symptoms of the disease or condition, a slower progression of the disease or condition, an improvement in the overall health or well-being of the subject, a reduction in infection, or by other parameters well known in the art that are specific to the particular disease or condition.

In some embodiments, an immune response induced by administering an effective amount of an ebolavirus GP peptide immunogen as disclosed herein inhibits infection of a human subject by ebolaviruses, for example, by at least 50% (such as at least 60%, at least 70%, at least 80%, at least 90%, or more) compared to a suitable control.

Isolated: An “isolated” biological component has been substantially separated or purified away from other biological components, such as other biological components in which the component naturally occurs, such as other chromosomal and extrachromosomal DNA, RNA, and proteins. Proteins, peptides, nucleic acids, and viruses that have been “isolated” include those purified by standard purification methods. Isolated does not require absolute purity, and can include protein, peptide, nucleic acid, or virus molecules that are at least 50% isolated, such as at least 75%, 80%, 90%, 95%, 98%, 99%, or even 99.9% isolated.

Linked: The term “linked” means joined together, either directly or indirectly. For example, a first moiety may be covalently or noncovalently (e.g., electrostatically) linked to a second moiety. This includes, but is not limited to, covalently bonding one molecule to another molecule, noncovalently bonding one molecule to another (e.g. electrostatically bonding), non-covalently bonding one molecule to another molecule by hydrogen bonding, non-covalently bonding one molecule to another molecule by van der Waals forces, and any and all combinations of such couplings. Indirect attachment is possible, such as by using a “linker”. In several embodiments, linked components are associated in a chemical or physical manner so that the components are not freely dispersible from one another, at least until contacting or entering a cell, such as an immune cell.

Linker: One or more molecules or groups of atoms positioned between two moieties. Typically, linkers are bifunctional, i.e., the linker includes a functional group at each end, wherein the functional groups are used to couple the linker to the two moieties. The two functional groups may be the same, i.e., a homobifunctional linker, or different, i.e., a heterobifunctional linker. In several embodiments, a peptide linker can be used to link the C-terminus of a first protein to the N-terminus of a second protein. Non-limiting examples of peptide linkers include glycine-serine peptide linkers, which are typically not more than 10 amino acids in length. Typically, such linkage is accomplished using molecular biology techniques to genetically manipulate DNA encoding the first polypeptide linked to the second polypeptide by the peptide linker.

Nucleic acid molecule: A polymeric form of nucleotides, which may include both sense and anti-sense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers of the above. A nucleotide refers to a ribonucleotide, deoxynucleotide or a modified form of either type of nucleotide. The term “nucleic acid molecule” as used herein is synonymous with “nucleic acid” and “polynucleotide.” A nucleic acid molecule is usually at least 10 bases in length, unless otherwise specified. The term includes single- and double-stranded forms of DNA. A polynucleotide may include either or both naturally occurring and modified nucleotides linked together by naturally occurring and/or non-naturally occurring nucleotide linkages. “cDNA” refers to a DNA that is complementary or identical to an mRNA, in either single stranded or double stranded form. “Encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom.

Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked nucleic acid sequences are contiguous and, where necessary to join two protein-coding regions, in the same reading frame.

Peptide: A polymer in which the monomers are amino acid residues that are joined together through amide bonds. The amino acids included in a peptide may be subject to post-translational modification (e.g., glycosylation or phosphorylation). A “residue” refers to an amino acid or amino acid mimetic incorporated in a peptide by an amide bond or amide bond mimetic. A peptide has an amino terminal (N-terminal) end and a carboxy terminal (C-terminal) end. In some embodiments, a peptide can In some embodiments, a peptide is at most 100 amino acids in length, such as at most 75 amino acids in length, such as at most 50 amino acids in length or at most 40 amino acids in length for example.

Peptide Modifications: Synthetic embodiments of the peptides described herein are also provided. For example, peptides can be modified by a variety of chemical techniques to produce derivatives having essentially the same activity as the unmodified peptides, and optionally having other desirable properties. For example, carboxylic acid groups of the peptide, whether carboxyl-terminal or side chain, can be provided in the form of a salt of a pharmaceutically-acceptable cation or esterified to form a C₁-C₁₆ ester, or converted to an amide of formula NR₁R₂ wherein R₁ and R₂ are each independently H or C₁-C₁₆ alkyl, or combined to form a heterocyclic ring, such as a 5- or 6-membered ring Amino groups of the peptide, whether amino-terminal or side chain, can be in the form of a pharmaceutically-acceptable acid addition salt, such as the HCl, HBr, acetic, benzoic, toluene sulfonic, maleic, tartaric and other organic salts, or can be modified to C₁-C₁₆ alkyl or dialkyl amino or further converted to an amide.

Hydroxyl groups of the peptide side chains may be converted to C1-C16 alkoxy or to a C1-C16 ester using well-recognized techniques. Phenyl and phenolic rings of the peptide side chains may be substituted with one or more halogen atoms, such as fluorine, chlorine, bromine or iodine, or with C1-C16 alkyl, C1-C16 alkoxy, carboxylic acids and esters thereof, or amides of such carboxylic acids. Methylene groups of the peptide side chains can be extended to homologous C₂-C₄ alkylenes. Thiols can be protected with any one of a number of well-recognized protecting groups, such as acetamide groups. Those skilled in the art will also recognize methods for introducing cyclic structures into the peptides of this invention to select and provide conformational constraints to the structure that result in enhanced stability.

Each peptide of this disclosure is comprised of a sequence of amino acids, which may be either L- and/or D-amino acids, naturally occurring and otherwise.

Pharmaceutically acceptable carriers: The pharmaceutically acceptable carriers of use are conventional. Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, Pa., 19th Edition, 1995, describes compositions and formulations suitable for pharmaceutical delivery of the disclosed immunogens.

In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (e.g., powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example, sodium acetate or sorbitan monolaurate. In particular embodiments, suitable for administration to a subject the carrier may be sterile, and/or suspended or otherwise contained in a unit dosage form containing one or more measured doses of the composition suitable to elicit the desired immune response. It may also be accompanied by medications for its use for treatment purposes. The unit dosage form may be, for example, in a sealed vial that contains sterile contents or a syringe for injection into a subject, or lyophilized for subsequent solubilization and administration or in a solid or controlled release dosage.

Prime-boost immunization: An immunotherapy including administration of multiple immunogens over a period of time to elicit the desired immune response.

Sequence identity: The similarity between amino acid sequences is expressed in terms of the similarity between the sequences, otherwise referred to as sequence identity. Sequence identity is frequently measured in terms of percentage identity; the higher the percentage, the more similar the two sequences are. Homologs, orthologs, or variants of a polypeptide will possess a relatively high degree of sequence identity when aligned using standard methods.

Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith & Waterman, Adv. Appl. Math. 2:482, 1981; Needleman & Wunsch, J. Mol. Biol. 48:443, 1970; Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988; Higgins & Sharp, Gene, 73:237-44, 1988; Higgins & Sharp, CABIOS 5:151-3, 1989; Corpet et al., Nuc. Acids Res. 16:10881-90, 1988; Huang et al. Computer Appls. in the Biosciences 8, 155-65, 1992; and Pearson et al., Meth. Mol. Bio. 24:307-31, 1994. Altschul et al., J. Mol. Biol. 215:403-10, 1990, presents a detailed consideration of sequence alignment methods and homology calculations.

Homologs and variants of a polypeptide are typically characterized by possession of at least about 75%, for example, at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity counted over the full length alignment with the amino acid sequence of interest. Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, such as at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity. When less than the entire sequence is being compared for sequence identity, homologs and variants will typically possess at least 80% sequence identity over short windows of 10-20 amino acids, and may possess sequence identities of at least 85% or at least 90% or 95% depending on their similarity to the reference sequence. Methods for determining sequence identity over such short windows are available at the NCBI website on the internet. These sequence identity ranges are provided for guidance only; it is entirely possible that strongly significant homologs could be obtained that fall outside of the ranges provided.

As used herein, reference to “at least 90% identity” (or similar language) refers to “at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or even 100% identity” to a specified reference sequence.

Specifically bind: When referring to the formation of an antibody:antigen protein complex, or a protein:protein complex, refers to a binding reaction which determines the presence of a target protein, peptide, or polysaccharide (for example, a glycoprotein), in the presence of a heterogeneous population of proteins and other biologics. Thus, under designated conditions, a particular antibody or protein binds preferentially to a particular target protein, peptide or polysaccharide (such as an antigen present on the surface of a pathogen) and does not bind in a significant amount to other proteins or polysaccharides present in the sample or subject. Specific binding can be determined by standard methods. A first protein or antibody specifically binds to a target protein when the interaction has a K_(D) of less than 10⁻⁶ Molar, such as less than 10⁻⁷ Molar, less than 10⁻⁸ Molar, less than 10⁻⁹, or even less than 10⁻¹⁰ Molar.

Subject: Living multicellular vertebrate organisms, a category that includes human and non-human mammals. In an example, a subject is a human. In an additional example, a subject is selected that is in need of inhibiting an ebolavirus infection. For example, the subject is uninfected and at risk of ebolavirus infection.

Under conditions sufficient for: A phrase that is used to describe any environment that permits a desired activity.

Vector: An entity containing a DNA or RNA molecule bearing a promoter(s) that is operationally linked to the coding sequence of an immunogenic protein of interest and can express the coding sequence. Non-limiting examples include a naked or packaged (lipid and/or protein) DNA, a naked or packaged RNA, a subcomponent of a virus or bacterium or other microorganism that may be replication-incompetent, or a virus or bacterium or other microorganism that may be replication-competent. A vector is sometimes referred to as a construct. Recombinant DNA vectors are vectors having recombinant DNA. A vector can include nucleic acid sequences that permit it to replicate in a host cell, such as an origin of replication. A vector can also include one or more selectable marker genes and other genetic elements. Viral vectors are recombinant nucleic acid vectors having at least some nucleic acid sequences derived from one or more viruses.

A non-limiting example of a DNA-based expression vector is pCDNA3.1, which can include includes a mammalian expression enhancer and promoter (such as a CMV promoter). Non-limiting examples of viral vectors include adeno-associated virus (AAV) vectors as well as Poxvirus vector (e.g., Vaccinia, MVA, avian Pox, or Adenovirus).

II. Filovirus GP Peptides

Isolated peptides containing fragments of filovirus GP proteins are disclosed herein that can be used to induce an immune response in a subject that neutralizes filovirus infection (such as Zaire ebolavirus infection. As discussed in the Examples, the isolated peptides contain antigenic sites of the filovirus GP that are targeted by neutralizing antibodies and are shown to induce an immune response in a subject that neutralizing filovirus infection (such as Zaire ebolavirus infection).

In several embodiments, the isolated peptides contain fragments of an ebolavirus GP, such as GP from one of Zaire ebolavirus, Bundibugyo ebolavirus, Sudan ebolavirus, or Tai Forest ebolavirus. Exemplary ebolavirus GP protein sequences are set forth herein as SEQ ID NOs: 34-41. In some embodiments, the isolated peptides contain fragments of a Marburg margburgvirus GP An exemplary Marburg margburgvirus GP protein sequence is set forth herein as SEQ ID NO: 42. In further embodiments, the isolated peptide contains a fragment of a GP from another Filovirus species.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of 10-100 consecutive amino acids or longer (such as 10-15, 10-20, 10-30, 10-40, 10-50, 20-30, 20-40, 20-50, 30-50, 40-50, 10-75, 20-75, 20-75, 20-75, 30-75, 40-75, 50-75, or 75-100 consecutive amino acids) from a native filovirus GP sequence, such as a GP sequence set forth as any one of SEQ ID NOs: 34-42. In some embodiments the isolated peptide is no more than 100 amino acids in length, such as no more than 75, or no more than 50, or no more than 40 amino acids in length.

The isolated peptide includes the amino acid sequence of an antigenic site of the filovirus GP. For example, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of any one of the antigenic sites of Zaire ebolavirus as set forth in FIG. 20, such as Antigenic site 11.1, 11.2, 11.3, 111.1, 111.2, IV.1, IV.2, IV.3, IV.4, IV.5, V.1, V.2, V.3, V.4, V.5, V.6, V.7, V.8, V.9. V.10, V.11, or VI. The sequences of antigenic sites shown in FIG. 20 correspond to the Zaire ebolavirus Mayinga GP sequence set forth as SEQ ID NO: 35. Due to the sequence homology of GP across filoviruses (see the filovirus GP sequence alignment provided in FIGS. 19A-19C), the antigenic sites provided in FIG. 20 can readily be identified in other filovirus GP sequences, for example, a GP from any of Zaire ebolavirus, Bundibugyo ebolavirus, Sudan ebolavirus, or Tai Forest ebolavirus, or Marburg margburgvirus, such as a GP protein sequence is set forth any one of SEQ ID NOs: 34-42, or other Filovirus strains

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site VI residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as SEQ ID NO: 9: KNITDKIX₁QIIHDFX₂DX₃X₄LPX₅QX₆X₇X₈X₉NWW, wherein X₁ is D or N, X₂ is V or I, X₃ is K or N, X₄ is T, P, or N, X₅ is D or N, X₆ is G, T, D, or N, X₇ is D or N, X₈ is N, D, or G, and X₉ is D or S, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NO: 9 is a consensus amino acid sequence encompassing the amino acids of antigenic site VI from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus. For example, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 10-13. In further embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site VI from a Margurg Marburgvirus, such as the Antigenic site VI sequence set forth as SEQ ID NO: 53.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as SEQ ID NO: 7: KNITDKIX₁QIIHDFX₂DX₃X₄LPX₅QX₆X₇X₈X₉NWWT, wherein: X₁ is D or N, X₂ is V and I, X₃ is K or N, X₄ is T, P, or N, X₅ is D or N, X₆ is G, T, D, or N, X₇ is D or N, X₈ is N, D, or G; and X₉ is D or S, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NO: 7 is a consensus amino acid sequence encompassing the amino acids of antigenic site VI from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus. For example, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 4, or 14-16. In further embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site VI from a Margurg Marburgvirus, such as the Antigenic site VI sequence set forth as SEQ ID NO: 54.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site VIA residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as SEQ ID NO: 6 (FX₂DX₃X₄LPX₅QX₆X₇X₈X₉NWWT, wherein: X₂ is selected from V and I; X₃ from K and N; X₄ from T, P, and N; X₅ and X₇ from D and N; X₆ from G, T, D, and N; X₈ from N, D, and G; and X₉ from D and S, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NO: 6 is a consensus amino acid sequence encompassing a C-terminal portion of antigenic site VIA from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus. For example, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 5, or residues 14-30 of SEQ ID NOs: 14-16 or 54.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site IV.1 residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 17-20, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NOs: 17-20 encompass the amino acids of antigenic site IV.1 from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus or other Filoviruses. In further embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site VI from a Margurg Marburgvirus, such as the Antigenic site IV.1 sequence set forth as SEQ ID NO: 58.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site V.1 residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 21-25, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NOs: 21-25 encompass the amino acids of antigenic site V.1 from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus or other Filoviruses. In further embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site VI from a Margurg Marburgvirus, such as the Antigenic site V.1 sequence set forth as SEQ ID NO: 59.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site V.6 residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 2, 26-28, or 43-46 wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NOs: 2, 26-28, and 43-46 encompass the amino acids of antigenic site V.6 from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus or other Filoviruses. In further embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site VI from a Margurg Marburgvirus, such as the Antigenic site V.6 sequence set forth as SEQ ID NO: 56.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site V.7 residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 3 or 32-34, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NOs: 3 and 32-34 encompass the amino acids of antigenic site V.7 from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus or other Filoviruses. In further embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site V.7 from a Margurg Marburgvirus, such as the Antigenic site VI sequence set forth as SEQ ID NO: 55.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site V.10 residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 29-31, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NOs: 29-31 encompass the amino acids of antigenic site V.10 from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus or other Filoviruses. In further embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site V.10 from a Margurg Marburgvirus, such as the Antigenic site VI sequence set forth as SEQ ID NO: 60.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of a portion of antigenic site V residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as SEQ ID NO: 8: TX₁₀EDHKIMASENSSAMVQVHSQGRX₁₁AAVSH wherein: X₁₀ is T or N; and X₁₁ is E or K, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NO: 8 is a consensus amino acid sequence including a portion of antigenic site V from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus. For example, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as SEQ ID NO: 1.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of antigenic site II.1 residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 47-50, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NOs: 47-50 encompass the amino acids of antigenic site II.1 from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus or other Filoviruses. In further embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site VI from a Margurg Marburgvirus, such as the Antigenic site II.1 sequence set forth as SEQ ID NO: 61.

In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site IV.2 residues from a filovirus GP, such as an ebolavirus GP or Marburgvirus GP. In some embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence set forth as any one of SEQ ID NOs: 51-52, wherein the peptide is no more than 100 (such as no more than 75, 50, 40, or 30) amino acids in length and induces a neutralizing immune response to filovirus (such as ebolavirus) in a subject. SEQ ID NOs: 51-51 encompass the amino acids of antigenic site IV.2 from GP of Zaire ebolavirus (Mayinga, Kikwit, and Makona), Bundibugyo ebolavirus, Sudan ebolavirus, and Tai Forest ebolavirus or other Filoviruses. In further embodiments, the isolated peptide comprises, consists essentially of, or consists of the amino acid sequence of the antigenic site VI from a Margurg Marburgvirus, such as the Antigenic site IV.2 sequence set forth as SEQ ID NO: 62.

Any of the isolated peptides disclosed herein can be conjugated to a carrier molecule, for example, to enhance the immune response in a subject to the peptide. The peptide can be directly conjugated to the carrier or indirectly via a linker.

In some examples, the peptide and the carrier are linked by a linker between a lysine amino acid residue present on the carrier protein and a cysteine amino acid residue fused (by a peptide bond) to the C-terminal residue of the peptide.

Suitable linkers include, but are not limited to, straight or branched-chain carbon linkers, heterocyclic carbon linkers or peptide linkers. For an immunogenic conjugate from two or more constituents, each of the constituents will contain the necessary reactive groups. Representative combinations of such groups are amino with carboxyl to form amide linkages or carboxy with hydroxyl to form ester linkages or amino with alkyl halides to form alkylamino linkages or thiols with thiols to form disulfides or thiols with maleimides or alkylhalides to form thioethers. Hydroxyl, carboxyl, amino and other functionalities, where not present may be introduced by known methods. Likewise, a wide variety of linking groups may be employed. In some cases, the linking group can be designed to be either hydrophilic or hydrophobic in order to enhance the desired binding characteristics of the peptide and the carrier. The covalent linkages should be stable relative to the solution conditions under which the conjugate is subjected.

In some embodiments, the linkers may be joined to the constituent amino acids through their side chains (such as through a disulfide linkage to cysteine) or to the alpha carbon, amino, and/or carboxyl groups of the terminal amino acids. In some embodiments, the linker, the peptide, and the carrier can be encoded as a single peptide such that the peptide and the carrier are joined by peptide bonds.

The procedure for attaching a carrier molecule to a peptide varies according to the chemical structure of the molecules. Peptides typically contain a variety of functional groups; for example, carboxylic acid (COOH), free amine (−NH₂) or sulfhydryl (—SH) groups, which are available for reaction with a suitable functional group on a peptide. Alternatively, the peptide is derivatized to expose or attach additional reactive functional groups. The derivatization may involve attachment of any of a number of linker molecules such as those available from Pierce Chemical Company, Rockford, Ill.

In some embodiments, a sulfosuccinimidyl (4-iodoacetyl)aminobenzoate (Sulfo-SIAB) linker is used to link the peptide to carrier. In some embodiments an m-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) linker is used to attach the peptide to carrier.

Any specific combination of peptide and carrier may be selected from the specific peptides and carrier that are listed herein.

It can be advantageous to produce conjugates in which more than one peptide as described herein is conjugated to a single carrier protein. In several embodiments, the conjugation of multiple peptides to a single carrier protein is possible because the carrier protein has multiple lysine or cysteine side-chains that can serve as sites of attachment. The amount of peptide reacted with the amount of carrier may vary depending upon the specific peptide and the carrier. In some embodiments, from 1 to 30, such as about 1, about 5, about 10, about 15, about 20, or about 30 peptides, or more, can be linked to each carrier protein molecule. In some embodiments (such as when KLH is used as a carrier, from 1 to 1000, such as about 10, about 20, about 30, about 40, about 50, about 100, about 200, about 300, about 400, about 500, about 700, or about 1000 peptides can be linked to each carrier protein molecule. “About” in this context refers to plus or minus 5% when measuring an average number of X peptide molecules per carrier molecule in the conjugate.

Examples of suitable carriers are those that can increase the immunogenicity of the conjugate and/or elicit antibodies against the carrier which are diagnostically, analytically, and/or therapeutically beneficial. Useful carriers include polymeric carriers, which can be natural, recombinantly produced, semi-synthetic or synthetic materials containing one or more amino groups, such as those present in a lysine amino acid residue present in the carrier, to which a reactant moiety can be attached. Carriers that fulfill these criteria are available (see, for example, Fattom et al., Infect. Immun. 58:2309-12, 1990; Devi et al., PNAS 88:7175-79, 1991; Szu et al., Infect. Immun. 59:4555-61, 1991; Szu et al., J. Exp. Med. 166:1510-24, 1987; and Pavliakova et al., Infect. Immun. 68:2161-66, 2000). A carrier can be useful even if the antibody that it elicits is not of benefit by itself.

Specific, non-limiting examples of suitable polypeptide carriers include, but are not limited to, natural, semi-synthetic or synthetic polypeptides or proteins from bacteria or viruses. In one embodiment, bacterial products for use as carriers include bacterial toxins. Bacterial toxins include bacterial products that mediate toxic effects, inflammatory responses, stress, shock, chronic sequelae, or mortality in a susceptible host. Specific, non-limiting examples of bacterial toxins include, but are not limited to: B. anthracis PA (for example, as encoded by bases 143779 to 146073 of GENBANK® Accession No. NC 007322); B. anthracis LF (for example, as encoded by the complement of bases 149357 to 151786 of GENBANK® Accession No. NC 007322); bacterial toxins and toxoids, such as tetanus toxin/toxoid (for example, as described in U.S. Pat. Nos. 5,601,826 and 6,696,065); diphtheria toxin/toxoid (for example, as described in U.S. Pat. Nos. 4,709,017 and 6,696,065), such as tetanus toxin heavy chain C fragment; P. aeruginosa exotoxin/toxoid (for example, as described in U.S. Pat. Nos. 4,428,931, 4,488,991 and 5,602,095); pertussis toxin/toxoid (for example, as described in U.S. Pat. Nos. 4,997,915, 6,399,076 and 6,696,065); and C. perfringens exotoxin/toxoid (for example, as described in U.S. Pat. Nos. 5,817,317 and 6,403,094) C. difficile toxin B or A, or analogs or mimetics of and combinations of two or more thereof. Viral proteins, such as hepatitis B surface antigen (for example, as described in U.S. Pat. Nos. 5,151,023 and 6,013,264) and core antigen (for example, as described in U.S. Pat. Nos. 4,547,367 and 4,547,368) can also be used as carriers, as well as proteins from higher organisms such as keyhole limpet hemocyanin (KLH), horseshoe crab hemocyanin, Concholepas Concholepas Hemocyanin (CCH), Ovalbumin (OVA), edestin, mammalian serum albumins (such as bovine serum albumin), and mammalian immunoglobulins. In some examples, the carrier is bovine serum albumin.

In some embodiments, the carrier is selected from one of: Keyhole Limpet Hemocyanin (KLH), tetanus toxoid, tetanus toxin heavy chain C fragment, diphtheria toxoid, diphtheria toxin variant CRM197, or H influenza protein D (HiD). CRM197 is a genetically detoxified form of diphtheria toxin; a single mutation at position 52, substituting glutamic acid for glycine, causes the ADP-ribosyltransferase activity of the native diphtheria toxin to be lost. For description of protein carriers for vaccines, see Pichichero, Protein carriers of conjugate vaccines: characteristics, development, and clinical trials, Hum Vaccin Immunother., 9: 2505-2523,2013, which is incorporated by reference herein in its entirety).

Following conjugation of the peptide to the carrier protein, the conjugate can be purified by appropriate techniques. One goal of the purification step is to separate the unconjugated peptide or carrier from the conjugate. One method for purification, involving ultrafiltration in the presence of ammonium sulfate, is described in U.S. Pat. No. 6,146,902. Alternatively, the conjugates can be purified away from unconjugated peptide or carrier by any number of standard techniques including, for example, size exclusion chromatography, density gradient centrifugation, hydrophobic interaction chromatography, or ammonium sulfate fractionation. See, for example, Anderson et al., J. Immunol. 137:1181-86, 1986 and Jennings & Lugowski, J. Immunol. 127:1011-18, 1981. The compositions and purity of the conjugates can be determined by GLC-MS and MALDI-TOF spectrometry, for example.

In several embodiments, the disclosed immunogenic conjugates can be formulated into an immunogenic composition (such as vaccines), for example by the addition of a pharmaceutically acceptable carrier and/or adjuvant.

III. Polynucleotides and Expression

Polynucleotides encoding the disclosed peptides are also provided. These polynucleotides include DNA, cDNA and RNA sequences which encode the peptide. The genetic code can be used to construct a variety of functionally equivalent nucleic acids, such as nucleic acids that differ in sequence but which encode the same protein sequence.

Exemplary nucleic acids can be prepared by cloning techniques. Examples of appropriate cloning and sequencing techniques, and instructions sufficient to direct persons of skill through many cloning exercises are known (see, e.g., Sambrook et al. (Molecular Cloning: A Laboratory Manual, 4^(th) ed, Cold Spring Harbor, N.Y., 2012) and Ausubel et al. (In Current Protocols in Molecular Biology, John Wiley & Sons, New York, through supplement 104, 2013).

Nucleic acids can also be prepared by amplification methods Amplification methods include polymerase chain reaction (PCR), the ligase chain reaction (LCR), the transcription-based amplification system (TAS), the self-sustained sequence replication system (3SR). A wide variety of cloning methods, host cells, and in vitro amplification methodologies are well known to persons of skill.

The polynucleotides encoding a disclosed peptide can include a recombinant DNA which is incorporated into a vector into an autonomously replicating plasmid or virus or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (such as a cDNA) independent of other sequences. The nucleotides can be ribonucleotides, deoxyribonucleotides, or modified forms of either nucleotide. The term includes single and double forms of DNA.

Polynucleotide sequences encoding a disclosed peptide can be operatively linked to expression control sequences. An expression control sequence operatively linked to a coding sequence is ligated such that expression of the coding sequence is achieved under conditions compatible with the expression control sequences. The expression control sequences include, but are not limited to, appropriate promoters, enhancers, transcription terminators, a start codon (i.e., ATG) in front of a protein-encoding gene, splicing signals for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons.

DNA sequences encoding the disclosed peptide can be expressed in vitro by DNA transfer into a suitable host cell. The cell may be prokaryotic or eukaryotic. The term also includes any progeny of the subject host cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. Methods of stable transfer, meaning that the foreign DNA is continuously maintained in the host, are known in the art.

Hosts can include microbial, yeast, insect and mammalian organisms. Methods of expressing DNA sequences having eukaryotic or viral sequences in prokaryotes are well known in the art. Non-limiting examples of suitable host cells include bacteria, archea, insect, fungi (for example, yeast), plant, and animal cells (for example, mammalian cells, such as human) Exemplary cells of use include Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Salmonella typhimurium, SF9 cells, C129 cells, 293 cells, Neurospora, and immortalized mammalian myeloid and lymphoid cell lines. Techniques for the propagation of mammalian cells in culture are well-known (see, e.g., Helgason and Miller (Eds.), 2012, Basic Cell Culture Protocols (Methods in Molecular Biology), 4^(th) Ed., Humana Press). Examples of commonly used mammalian host cell lines are VERO and HeLa cells, CHO cells, and WI38, BHK, and COS cell lines, although cell lines may be used, such as cells designed to provide higher expression, desirable glycosylation patterns, or other features. In some embodiments, the host cells include HEK293 cells or derivatives thereof, such as GnTI^(−/−) cells (ATCC® No. CRL-3022), or HEK-293F cells.

Transformation of a host cell with recombinant DNA can be carried out by conventional techniques. In some embodiments, if the host is prokaryotic, such as, but not limited to, E. coli, competent cells which are capable of DNA uptake can be prepared from cells harvested after exponential growth phase and subsequently treated by the CaCl₂ method. Alternatively, MgCl₂ or RbCl can be used. Transformation can also be performed after forming a protoplast of the host cell if desired, or by electroporation.

When the host is a eukaryote, such methods of transfection of DNA as calcium phosphate coprecipitates, conventional mechanical procedures such as microinjection, electroporation, insertion of a plasmid encased in liposomes, or viral vectors can be used. Eukaryotic cells can also be co-transformed with polynucleotide sequences encoding a disclosed antigen, and a second foreign DNA molecule encoding a selectable phenotype, such as the herpes simplex thymidine kinase gene. Another method is to use a eukaryotic viral vector, such as simian virus 40 (SV40) or bovine papilloma virus, to transiently infect or transform eukaryotic cells and express the protein (see for example, Viral Expression Vectors, Springer press, Muzyczka ed., 2011). Appropriate expression systems such as plasmids and vectors of use in producing proteins in cells including higher eukaryotic cells such as the COS, CHO, HeLa and myeloma cell lines can be utilized.

Modifications can be made to a nucleic acid encoding a disclosed peptide without diminishing its biological activity. Some modifications can be made to facilitate the cloning, expression, or incorporation of the peptide into a fusion protein. Non-limiting examples of such modifications include termination codons, a methionine added at the amino terminus to provide an initiation site, additional amino acids placed on either terminus to create conveniently located restriction sites, or additional amino acids (such as poly His) to aid in purification steps.

IV. Viral Vectors

A nucleic acid molecule encoding a disclosed peptide can be included in a viral vector, for example, for expression of the immunogen in a host cell, or for immunization of a subject as disclosed herein. In some embodiments, the viral vectors are administered to a subject as part of a prime-boost immunization. In several embodiments, the viral vectors used in a prime-boost immunization protocol to prime an immune response to ebolavirus GP or boost an immune response to ebolavirus GP.

In several examples, the viral vector can be replication-competent. For example, the viral vector can have a mutation in the viral genome that does not inhibit viral replication in host cells. The viral vector also can be conditionally replication-competent. In other examples, the viral vector is replication-deficient in host cells.

A number of viral vectors have been constructed that can be used to express the disclosed antigens, including polyoma, i.e., SV40 (Madzak et al., 1992, J. Gen. Virol., 73:15331536), adenovirus (Berkner, 1992, Cur. Top. Microbiol. Immunol., 158:39-6; Berliner et al., 1988, Bio Techniques, 6:616-629; Gorziglia et al., 1992, J. Virol., 66:4407-4412; Quantin et al., 1992, Proc. Natl. Acad. Sci. USA, 89:2581-2584; Rosenfeld et al., 1992, Cell, 68:143-155; Wilkinson et al., 1992, Nucl. Acids Res., 20:2233-2239; Stratford-Perricaudet et al., 1990, Hum. Gene Ther., 1:241-256), vaccinia virus (Mackett et al., 1992, Biotechnology, 24:495-499), adeno-associated virus (Muzyczka, 1992, Curr. Top. Microbiol. Immunol., 158:91-123; On et al., 1990, Gene, 89:279-282), herpes viruses including HSV and EBV (Margolskee, 1992, Curr. Top. Microbiol. Immunol., 158:67-90; Johnson et al., 1992, J. Virol., 66:29522965; Fink et al., 1992, Hum. Gene Ther. 3:11-19; Breakfield et al., 1987, Mol. Neurobiol., 1:337-371; Fresse et al., 1990, Biochem. Pharmacol., 40:2189-2199), Sindbis viruses (H. Herweijer et al., 1995, Human Gene Therapy 6:1161-1167; U.S. Pat. Nos. 5,091,309 and 5,2217,879), alphaviruses (S. Schlesinger, 1993, Trends Biotechnol. 11:18-22; I. Frolov et al., 1996, Proc. Natl. Acad. Sci. USA 93:11371-11377) and retroviruses of avian (Brandyopadhyay et al., 1984, Mol. Cell Biol., 4:749-754; Petropouplos et al., 1992, J. Virol., 66:3391-3397), murine (Miller, 1992, Curr. Top. Microbiol. Immunol., 158:1-24; Miller et al., 1985, Mol. Cell Biol., 5:431-437; Sorge et al., 1984, Mol. Cell Biol., 4:1730-1737; Mann et al., 1985, J. Virol., 54:401-407), and human origin (Page et al., 1990, J. Virol., 64:5370-5276; Buchschalcher et al., 1992, J. Virol., 66:2731-2739). Baculovirus (Autographa californica multinuclear polyhedrosis virus; AcMNPV) vectors are also known in the art, and may be obtained from commercial sources (such as PharMingen, San Diego, Calif.; Protein Sciences Corp., Meriden, Conn.; Stratagene, La Jolla, Calif.).

VI. Immunogenic Compositions

Immunogenic compositions comprising a disclosed peptide (for example, linked to a carrier) or a nucleic acid molecule or vector encoding the peptide and a pharmaceutically acceptable carrier are also provided. Such compositions can be administered to subjects by a variety of administration modes, for example, intramuscular, subcutaneous, intravenous, intra-arterial, intra-articular, intraperitoneal, or parenteral routes. Actual methods for preparing administrable compositions are described in more detail in such publications as Remingtons Pharmaceutical Sciences, 19^(th) Ed., Mack Publishing Company, Easton, Pa., 1995.

The peptide (for example, linked to a carrier) or a nucleic acid molecule or vector encoding the peptide can be formulated with pharmaceutically acceptable carriers to help retain biological activity while also promoting increased stability during storage within an acceptable temperature range. Potential carriers include, but are not limited to, physiologically balanced culture medium, phosphate buffer saline solution, water, emulsions (e.g., oil/water or water/oil emulsions), various types of wetting agents, cryoprotective additives or stabilizers such as proteins, peptides or hydrolysates (e.g., albumin, gelatin), sugars (e.g., sucrose, lactose, sorbitol), amino acids (e.g., sodium glutamate), or other protective agents. The resulting aqueous solutions may be packaged for use as is or lyophilized. Lyophilized preparations are combined with a sterile solution prior to administration for either single or multiple dosing.

Formulated compositions, especially liquid formulations, may contain a bacteriostat to prevent or minimize degradation during storage, including but not limited to effective concentrations (usually ≤1% w/v) of benzyl alcohol, phenol, m-cresol, chlorobutanol, methylparaben, and/or propylparaben. A bacteriostat may be contraindicated for some patients; therefore, a lyophilized formulation may be reconstituted in a solution either containing or not containing such a component.

The immunogenic compositions of the disclosure can contain as pharmaceutically acceptable vehicles substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, and triethanolamine oleate.

The immunogenic composition may optionally include an adjuvant to enhance an immune response of the host. Suitable adjuvants are, for example, toll-like receptor agonists, alum, AlPO4, alhydrogel, Lipid-A and derivatives or variants thereof, oil-emulsions, saponins, neutral liposomes, liposomes containing the vaccine and cytokines, non-ionic block copolymers, and chemokines. Non-ionic block polymers containing polyoxyethylene (POE) and polyxylpropylene (POP), such as POE-POP-POE block copolymers, MPL™ (3-O-deacylated monophosphoryl lipid A; Corixa, Hamilton, Ind.) and IL-12 (Genetics Institute, Cambridge, Mass.) may also be used as an adjuvant (Newman et al., 1998, Critical Reviews in Therapeutic Drug Carrier Systems 15:89-142). These adjuvants have the advantage in that they help to stimulate the immune system in a non-specific way, thus enhancing the immune response to a pharmaceutical product.

In some embodiments, the immunogenic composition can be provided as a sterile composition. The immunogenic composition typically contains an effective amount of a disclosed peptide (for example, linked to a carrier) or a nucleic acid molecule or vector encoding the peptide, and can be prepared by conventional techniques. Typically, the amount of a disclosed peptide (for example, linked to a carrier) or a nucleic acid molecule or vector encoding the peptide in each dose of the immunogenic composition is selected as an amount which elicits an immune response without significant, adverse side effects. In some embodiments, the immunogenic composition can be provided in unit dosage form for use to elicit an immune response in a subject, for example, to prevent ebolavirus infection in the subject. A unit dosage form contains a suitable single preselected dosage for administration to a subject, or suitable marked or measured multiples of two or more preselected unit dosages, and/or a metering mechanism for administering the unit dose or multiples thereof. In other embodiments, the composition further includes an adjuvant.

VII. Methods of Inducing an Immune Response

An immunogenic composition comprising a disclosed filovirus GP (e.g., Zaire ebolavirus GP) peptide, a nucleic acid molecule (such as an RNA molecule) encoding a disclosed filovirus GP (e.g., Zaire ebolavirus GP) peptide, vector including the nucleic acid molecule, or immunogenic composition, can be administered to a subject to induce an immune response to filovirus GP (e.g., Zaire ebolavirus GP) in the subject. In a particular example, the subject is a human. The immune response can be a protective immune response, for example a response that inhibits subsequent infection with a filovirus (such as a Zaire ebolavirus). Elicitation of the immune response can also be used to treat or inhibit infection and illnesses associated with a filovirus (such as a Zaire ebolavirus).

A subject can be selected for immunization that has, or is at risk for developing infection or illness associated with a filovirus (such as a Zaire ebolavirus), for example because of exposure or the possibility of exposure to a filovirus (such as a Zaire ebolavirus).

Typical subjects intended for administration of the immunogenic composition include humans, as well as non-human primates and other animals. To identify relevant subjects, accepted screening methods are employed to determine risk factors associated with a targeted or suspected disease or condition, or to determine the status of an existing disease or condition in a subject. These screening methods include, for example, conventional work-ups to determine environmental, familial, occupational, and other such risk factors that may be associated with the targeted or suspected disease or condition, as well as diagnostic methods, such as various ELISA and other immunoassay methods to detect and/or characterize a filovirus (such as a Zaire ebolavirus) infection. These and other routine methods allow the clinician to select patients in need of therapy. In accordance with these methods and principles, the immunogenic composition can be administered according to the teachings herein, or other conventional methods, as an independent prophylaxis or treatment program, or as a follow-up, adjunct or coordinate treatment regimen to other treatments.

The administration of the immunogenic composition can be for prophylactic or therapeutic purpose. When provided prophylactically, the immunogenic composition can be provided in advance of any symptom, for example, in advance of infection. The prophylactic administration serves to prevent or ameliorate any subsequent infection. In some embodiments, the methods can involve selecting a subject at risk for contracting filovirus infection (e.g., Zaire ebolavirus infection), and administering an effective amount of the immunogenic composition to the subject. The immunogenic composition can be provided prior to the anticipated exposure to filovirus infection (e.g., Zaire ebolavirus infection) so as to attenuate the anticipated severity, duration or extent of an infection and/or associated disease symptoms, after exposure or suspected exposure to the virus, or after the actual initiation of an infection.

The immunogenic composition is provided to the subject in an amount effective to induce or to enhance an immune response against filovirus GP (e.g., Zaire ebolavirus GP) in the subject, preferably a human. The actual dosage of the immunogenic composition will vary according to factors such as the disease indication and particular status of the subject (for example, the subject's age, size, fitness, extent of symptoms, susceptibility factors, and the like), time and route of administration, other drugs or treatments being administered concurrently, as well as the specific pharmacology of the composition for eliciting the desired activity or biological response in the subject. Dosage regimens can be adjusted to provide an optimum prophylactic or therapeutic response.

An immunogenic composition including one or more of the disclosed immunogens can be used in coordinate (or prime-boost) vaccination protocols or combinatorial formulations. In certain embodiments, novel combinatorial immunogenic compositions and coordinate immunization protocols employ separate immunogens or formulations, each directed toward eliciting an anti-viral immune response, such as an immune response to filovirus GP (e.g., Zaire ebolavirus GP). Separate immunogenic compositions that elicit the anti-viral immune response can be combined in a polyvalent immunogenic composition administered to a subject in a single immunization step, or they can be administered separately (in monovalent immunogenic compositions) in a coordinate (or prime-boost) immunization protocol.

There can be several boosts, and each boost can be a different disclosed immunogen. In some examples that the boost may be the same immunogen as another boost, or the prime. The prime and boost can be administered as a single dose or multiple doses, for example two doses, three doses, four doses, five doses, six doses or more can be administered to a subject over days, weeks or months. Multiple boosts can also be given, such one to five (e.g., 1, 2, 3, 4 or 5 boosts), or more. Different dosages can be used in a series of sequential immunizations. For example a relatively large dose in a primary immunization and then a boost with relatively smaller doses.

In some embodiments, the boost can be administered about two, about three to eight, or about four, weeks following the prime, or about several months after the prime. In some embodiments, the boost can be administered about 5, about 6, about 7, about 8, about 10, about 12, about 18, about 24, months after the prime, or more or less time after the prime. Periodic additional boosts can also be used at appropriate time points to enhance the subject's “immune memory.” The adequacy of the vaccination parameters chosen, e.g., formulation, dose, regimen and the like, can be determined by taking aliquots of serum from the subject and assaying antibody titers during the course of the immunization program. In addition, the clinical condition of the subject can be monitored for the desired effect, e.g., inhibition of filovirus infection (e.g., Zaire ebolavirus infection) or improvement in disease state (e.g., reduction in viral load). If such monitoring indicates that vaccination is sub-optimal, the subject can be boosted with an additional dose of immunogenic composition, and the vaccination parameters can be modified in a manner expected to potentiate the immune response.

In some embodiments, the prime-boost method can include DNA-prime and protein-boost vaccination protocol to a subject. The method can include two or more administrations of the nucleic acid molecule or the protein.

For peptide therapeutics, typically, each human dose will comprise 1-1000 μg of protein, such as from about 1 μg to about 100 μg, for example, from about 1 μg to about 50 μg, such as about 1 μg, about 2 μg, about 5 μg, about 10 μg, about 15 μg, about 20 μg, about 25 μg, about 30 μg, about 40 μg, or about 50 μg.

The amount utilized in an immunogenic composition is selected based on the subject population (e.g., infant or elderly). An optimal amount for a particular composition can be ascertained by standard studies involving observation of antibody titers and other responses in subjects. It is understood that an effective amount of a disclosed immunogenic composition can include an amount that is ineffective at eliciting an immune response by administration of a single dose, but that is effective upon administration of multiple dosages, for example in a prime-boost administration protocol.

Upon administration of the immunogenic composition, the immune system of the subject typically responds to the immunogenic composition by producing antibodies specific for viral protein. Such a response signifies that an immunologically effective dose was delivered to the subject.

In some embodiments, the antibody response of a subject will be determined in the context of evaluating effective dosages/immunization protocols. In most instances it will be sufficient to assess the antibody titer in serum or plasma obtained from the subject. Decisions as to whether to administer booster inoculations and/or to change the amount of the therapeutic agent administered to the individual can be at least partially based on the antibody titer level. The antibody titer level can be based on, for example, an immunobinding assay which measures the concentration of antibodies in the serum which bind to an antigen including, for example, filovirus GP (e.g., Zaire ebolavirus GP).

Filovirus infection (e.g., Zaire ebolavirus infection) does not need to be completely eliminated or reduced or prevented for the methods to be effective. For example, elicitation of the immune response can reduce or inhibit infection with the Filovirus (e.g., Zaire ebolavirus) by a desired amount, for example, by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable infected cells), as compared to infection with the Filovirus (e.g., Zaire ebolavirus) in the absence of the immunization.

One approach to administration of nucleic acids is direct immunization with plasmid DNA, such as with a mammalian expression plasmid Immunization by nucleic acid constructs is well known in the art and taught, for example, in U.S. Pat. No. 5,643,578 (which describes methods of immunizing vertebrates by introducing DNA encoding a desired antigen to elicit a cell-mediated or a humoral response), and U.S. Pat. Nos. 5,593,972 and 5,817,637 (which describe operably linking a nucleic acid sequence encoding an antigen to regulatory sequences enabling expression). U.S. Pat. No. 5,880,103 describes several methods of delivery of nucleic acids encoding immunogenic peptides or other antigens to an organism. The methods include liposomal delivery of the nucleic acids (or of the synthetic peptides themselves), and immune-stimulating constructs, or ISCOMS™, negatively charged cage-like structures of 30-40 nm in size formed spontaneously on mixing cholesterol and Quil A™ (saponin). Protective immunity has been generated in a variety of experimental models of infection, including toxoplasmosis and Epstein-Barr virus-induced tumors, using ISCOMS™ as the delivery vehicle for antigens (Mowat and Donachie, Immunol. Today 12:383, 1991). Doses of antigen as low as 1 μg encapsulated in ISCOMS™ have been found to produce Class I mediated CTL responses (Takahashi et al., Nature 344:873, 1990).

In some embodiments, a plasmid DNA vaccine is used to express a disclosed filovirus GP peptide (e.g., Zaire ebolavirus GP peptide) in a subject. For example, a nucleic acid molecule encoding a disclosed filovirus GP peptide (e.g., Zaire ebolavirus GP peptide) can be administered to a subject to induce an immune response to filovirus GP (e.g., Zaire ebolavirus GP).

In another approach, a disclosed filovirus GP peptide (e.g., Zaire ebolavirus GP peptide) can be expressed by attenuated viral hosts or vectors or bacterial vectors. Recombinant vaccinia virus, adeno-associated virus (AAV), herpes virus, retrovirus, cytogmeglo virus or other viral vectors can be used to express the peptide or protein, thereby eliciting a CTL response. For example, vaccinia vectors and methods useful in immunization protocols are described in U.S. Pat. No. 4,722,848. BCG (Bacillus Calmette Guerin) provides another vector for expression of the peptides (see Stover, Nature 351:456-460, 1991). These peptides can also be used in combination or with vaccines against other pathogens.

In one embodiment, a nucleic acid encoding a disclosed filovirus GP peptide (e.g., Zaire ebolavirus GP peptide) is introduced directly into cells to induce the immune response. For example, the nucleic acid can be loaded onto gold microspheres by standard methods and introduced into the skin by a device such as Bio-Rad's HELIOS™ Gene Gun. The nucleic acids can be “naked,” consisting of plasmids under control of a strong promoter. Typically, the DNA is injected into muscle, although it can also be injected directly into other sites. Dosages for injection are usually around 0.5 μg/kg to about 50 mg/kg, and typically are about 0.005 mg/kg to about 5 mg/kg (see, e.g., U.S. Pat. No. 5,589,466).

In another embodiment, an mRNA-based immunization protocol can be used to deliver a nucleic acid encoding a disclosed filovirus GP peptide (e.g., Zaire ebolavirus GP peptide) directly into cells. In some embodiments, nucleic acid-based vaccines based on mRNA may provide a potent alternative to the previously mentioned approaches. mRNA vaccines preclude safety concerns about DNA integration into the host genome and can be directly translated in the host cell cytoplasm. Moreover, the simple cell-free, in vitro synthesis of RNA avoids the manufacturing complications associated with viral vectors. Two exemplary forms of RNA-based vaccination that can be used to deliver a nucleic acid encoding a disclosed filovirus GP peptide (e.g., Zaire ebolavirus GP peptide) include conventional non-amplifying mRNA immunization (see, e.g., Petsch et al., “Protective efficacy of in vitro synthesized, specific mRNA vaccines against influenza A virus infection,” Nature biotechnology, 30(12):1210-6, 2012) and self-amplifying mRNA immunization (see, e.g., Geall et al., “Nonviral delivery of self-amplifying RNA vaccines,” PNAS, 109(36): 14604-14609, 2012; Magini et al., “Self-Amplifying mRNA Vaccines Expressing Multiple Conserved Influenza Antigens Confer Protection against Homologous and Heterosubtypic Viral Challenge,” PLoS One, 11(8):e0161193, 2016; and Brito et al., “Self-amplifying mRNA vaccines,” Adv Genet., 89:179-233, 2015).

In some embodiments, administration of an effective amount of one or more of the disclosed immunogens to a subject induces a neutralizing or protective immune response in the subject. To assess neutralization activity, following immunization of a subject, serum can be collected from the subject at appropriate time points, frozen, and stored for neutralization testing. Methods to assay for binding or neutralization activity are known to the person of ordinary skill in the art and are further described herein, and include, but are not limited to, ELISA, plaque reduction neutralization (PRNT) assays, microneutralization assays, flow cytometry based assays, single-cycle infection assays. In some embodiments, the serum neutralization activity can be assayed using a panel of filovirus (e.g., Zaire ebolavirus) pseudoviruses.

VIII. Methods of Detection and Diagnosis

Methods are also provided for the detection of the presence of antibodies to filovirus GP in a biological sample. The method can be used to identify a biological sample from a subject with a filovirus (such as ebolavirus) infection, or from a subject that had a prior infection with a filovirus (such as an ebolavirus). In one example, the presence of filovirus (for example, Zaire ebolavirus) GP is detected in a biological sample from a subject, and can be used to identify a subject with filovirus infection. The sample can be any sample form a subject that contains antibodies induced by the filovirus infection, including, but not limited to body fluids, such as blood, serum, plasma, sputum, spinal fluid or urine. The method of detection can include contacting the sample with an isolated filovirus peptide as disclosed herein and under conditions sufficient to form an immune complex between the peptide and the antibodies in the sample, and detecting the immune complex.

In some embodiments, the peptides disclosed herein are used to test vaccines. For example to test if a test vaccine elicits an immune response that targets a particular antigenic site on the filovirus GP, such as antigenic site VI of Zaire ebolavirus as disclosed herein. Such methods involve immunizing a subject with a vaccine, and then screening a sample from the subject that contains antibodies induced by the immunization for antibody binding to the appropriate peptide.

Thus, the peptides disclosed herein can be used for serodiagnosis as well as development of assays for evaluation of vaccine or therapeutics or countermeasures or effectivity of these approaches.

VIII. Additional Description of Certain Embodiments

The present disclosure provides an immunogenic composition for inducing an immune response. The present disclosure also relates to prophylactic uses of the immunogenic compositions, for use in eliciting antibodies to the immunogen. In certain embodiments, the present disclosure relates to immunogenic compositions that provide a method of treating or suppressing a Filovirus disease in a patient, the method comprising administering to a patient the immunogenic composition of the disclosure.

In certain embodiments, the present disclosure relates to an immunogenic composition comprising one or more peptide fragments of a filovirus protein for use in eliciting an immunogenic response in a mammal. In other embodiments, the immunogenic composition can further comprise carrier proteins conjugated to the peptide fragments. The immunogenic composition can further comprise an adjuvant.

In certain embodiments, the peptide fragment or peptide fragments comprise one or more of the amino acid sequences selected from the following group of amino acid sequences or variants thereof:

SEQ ID NO: 1:  TTEDHKIMASENSSAMVQVHSQGREAAVSH SEQ ID NO: 2:  ETAGNNNTHHQDTGEESASSGKLGLITN SEQ ID NO: 3:  TGEESASSGKLGLITNTIAGVAGLITGGRR SEQ ID NO: 4:  KNITDKIDQIIHDFVDKTLPDQGDNDNWWT SEQ ID NO: 5:  FVDKTLPDQGDNDNWWT SEQ ID NO: 6  (FX₂DX₃X₄TLPX₅QX₆X₇X₈X₉NWWT)  wherein: X₂ is selected from V and I;  X₃ from K and N; X₄ from T, P, and N;  X₅ and X₇ from D and N; X₆ from G, T, D, and N;  X₈ from N, D, and G; and X₉ from D and S. SEQ ID NO: 7   (KNITDKIXIQIIHDFX₂DX₃X₄TLPX₅QX₆X₇X₈X₉NVVWT) wherein: X₂ is selected from V and I; X₃ from K  and N; X₄ from T, P, and N; X₁, X₅ and X₇ from D  and N; X₆ from G, T, D, and N; X₈ from N, D, and  G; and X₉ from D and S. SEQ ID NO: 8  (TX₁₀EDHKIMASENSSAMVQVHSQGRX₁₁AAVSH)  wherein: X₁₀ is selected from T and N; and X₁₁  from E and K.

In certain embodiments, a non-limiting acceptable carrier molecule includes keyhole limpet hemocyanin (KLH), DNA vectors, lentiviral vectors, nanoparticles, vesicular stomatitis virus (VSV), bovine serum albumin, ovalbumin, fowl immunoglobulin, and cytosine-phosphate-guanine (CpG) oligodeoxynucleotides.

Clause 1. An immunogenic composition comprising a peptide fragment comprising an amino acid sequence of SEQ ID NO: 6 (FX₂DX₃X₄LPX₅QX₆X₇X₈X₉NWWT) wherein: X₂ is selected from V and I; X₃ from K and N; X₄ from T, P, and N; X₅ and X₇ from D and N; X₆ from G, T, D, and N; X₈ from N, D, and G; and X₉ from D and S.

Clause 2. The immunogenic composition of Clause 1 wherein the peptide fragment comprises the amino acid sequence SEQ ID NO:5 (FVDKTLPDQGDNDNWWT).

Clause 3. An immunogenic composition comprising a peptide fragment comprising an amino acid sequence of SEQ ID NO: 7 (KNITDKIX₁QIIHDFX₂DX₃X₄LPX₅QX₆X₇X₈X₉NWWT) wherein: X2 is selected from V and I; X₃ from K and N; X₄ from T, P, and N; X₁, X₅ and X₇ from D and N; X₆ from G, T, D, and N; X₈ from N, D, and G; and X₉ from D and S.

Clause 4. The immunogenic composition of Clause 3 wherein the peptide fragment comprises the amino acid sequence SEQ ID NO: 4 (KNITDKIDQIIHDFVDKTLPDQGDNDNWWT).

Clause 5. An immunogenic composition comprising a peptide fragment comprises an amino acid sequence of SEQ ID NO: 8 (TX₁₀EDHKIMASENSSAMVQVHSQGRX₁₁AAVSH) wherein: X₁₀ is selected from T and N; and X₁₁ from E and K.

Clause 6. The immunogenic composition of Clause 5 wherein the peptide fragment comprises the amino acid sequence SEQ ID NO: 1 (TTEDHKIMASENSSAMVQVHSQGREAAVSH).

Clause 7. An immunogenic composition comprising a peptide fragment comprising an amino acid sequence of SEQ ID NO: 2 (ETAGNNNTHHQDTGEESASSGKLGLITN).

Clause 8. An immunogenic composition comprising a peptide fragment comprising an amino acid sequence of SEQ ID NO: 3 (TGEESASSGKLGLITNTIAGVAGLITGGRR).

Clause 9. An immunogenic composition comprising a peptide fragment comprising an amino acid sequence of SEQ ID NO: 5 or SEQ ID NO: 6 and a peptide fragment or peptide fragments selected from the list of peptide fragments encoded by amino acid sequences SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 7, and SEQ ID NO: 8.

Clause 10. An immunogenic composition comprising a peptide fragment having amino acid sequence SEQ ID NO: 4 or SEQ ID NO: 7 and a peptide fragment or peptide fragments selected from the list of peptide fragments encoded by amino acid sequences SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 6, and SEQ ID NO: 8.

Clause 11. An immunogenic composition comprising a peptide fragment or peptide fragments selected from the list of peptide fragments encoded by the amino acid sequences SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8.

Clause 12. The immunogenic composition of Clauses 1-11 further comprising an adjuvant.

Clause 13. The immunogenic composition of Clause 12 where in the adjuvant is oil in water, CpG, or a carrier protein.

Clause 14. The immunogenic composition of Clauses 1-11 further comprising a carrier protein whereby the carrier protein is conjugated to each peptide fragment.

Clause 15. The immunogenic for composition of Clause 14 where in the carrier protein is keyhole limpet hemocyanin.

EXAMPLES

The following examples are provided to illustrate particular features of certain embodiments, but the scope of the claims should not be limited to those features exemplified.

Example 1 Human Antibody Repertoire after VSV-Ebola Vaccination Identifies Novel Targets and Virus-Neutralizing IgM Antibodies

Development of an effective vaccine against Ebola virus is of high priority. However, knowledge about potential correlates of protection and the durability of immune response after vaccination is limited. Here, we elucidate the human antibody repertoire after administration of vesicular stomatitis virus (VSV)-Ebola vaccine at 3 million, 20 million and 100 million plaque-forming units (PFU) and homologous VSV-Ebola vaccine boost in healthy adult volunteers. Whole genome-fragment phage display libraries, expressing linear and conformational epitopes of Ebola glycoprotein (GP), showed higher diversity of antibody epitopes in individuals vaccinated with 20 million PFU than in those vaccinated with 3 million or 100 million PFU. Surface plasmon resonance kinetics showed higher levels of GP-binding antibodies after a single vaccination with 20 million or 100 million PFU than with 3 million PFU, and these correlated strongly with neutralization titers. A second vaccination did not boost antibody or virus neutralization titers, which declined rapidly, and induced only minimal antibody affinity maturation. Isotype analysis revealed a predominant IgM response even after the second vaccination, which contributed substantially to virus neutralization in vitro. These findings may help identify new vaccine targets and aid development and evaluation of effective countermeasures against Ebola.

The recent 2014 epidemic of highly pathogenic Ebola virus (EBOV) in Western Africa caused tens of thousands of infections and deaths. With occasional small outbreaks of new cases in Western Africa and the possibility of long-term persistence of virus in some survivors, it is feared that future outbreaks could occur and lead to severe epidemics. Therefore, development of an effective vaccine against Ebola is a high priority, both for pre-epidemic preparedness and for rapid vaccination to control future outbreaks. Protection against EBOV disease is attributed, at least partially, to the humoral immune response, as passive transfer of antibodies to naive NHPs can protect recipients against lethal EBOV challenge. Diverse ELISA, EBOV neutralization tests and immune parameters have been used to identify the vaccine correlates of protection (Matassov, D. et al. J. Infect. Dis. 212 (Suppl. 2), S443-S451, 2015; Blaney, J. E. et al. PLoS Pathog. 9, e1003389, 2013; and Wong, G. et al. Sci. Transl. Med. 4, 158ra146, 2012). A recent study also investigated the role of T cells in EBOV-infected patients and found that expression of the inhibitory molecules cytotoxic T lymphocyte-associated protein 4 (CTLA-4) and programmed cell death protein 1 (PD-1) on CD4+ and CD8+ T cells was lower in survivors than in fatal cases (Ruibal, P. et al. Nature 533, 100-104, 2016). However, to date, no single assay has been found to be predictive of protection, and the correlation of antibody titers measured by various assays has not been clearly demonstrated. Coupled with the difficulty of conducting adequate randomized controlled trials to demonstrate vaccine effectiveness on the basis of clinical EBOV disease, it is important to identify and understand immune markers that are reasonably likely to predict clinical benefit and can facilitate evaluation of vaccine candidates.

Recently, a recombinant VSV (rVSV)-based vaccine expressing Ebola Zaire surface glycoprotein from the Kikwit 1995 strain (rVSVΔG-ZEBOV-GP) was reported to decrease transmission to close contacts in a ring vaccination study in Guinea (Henao-Restrepo, A. M. et al. Lancet 386, 857-866, 2015). Here we performed an in-depth comprehensive analysis of the humoral immune response after primary rVSVΔG-ZEBOV-GP vaccination administered at 3 million, 20 million or 100 million PFU and homologous rVSVΔG-ZEBOV-GP vaccine boost in healthy US adult volunteers in a phase 1 placebo-controlled trial (Regules, J. A. et al. N. Engl. J. Med. 376(4):330-341, 2017, available online Apr. 1, 2015). Polyclonal serum was analyzed quantitatively and qualitatively to elucidate antibody epitope repertoires using gene-fragment phage display libraries (GFPDLs) and surface plasmon resonance (SPR) technology to measure realtime antibody binding kinetics, antibody cross-reactivity, immunoglobulin isotypes, affinity maturation and antibody persistence in recipients of the rVSVΔG-ZEBOV-GP vaccine.

Results

Antibody Epitope Repertoire after Vaccination

A rVSVΔG-ZEBOV-GP vaccine was administered intramuscularly at 3 million, 20 million or 100 million PFU to 39 healthy adult volunteers at the US National Institute of Allergy and Infectious Diseases (NIAID). In each dosing cohort, ten people received active vaccine, and three received a saline placebo. Serum samples from each individual were collected before vaccination (day 0), after the first vaccination (day 28), after the second vaccination (days 42 and 56) and on days 84 and 180. To analyze the epitope repertoire of serum samples from participants who received the rVSVΔG-ZEBOV-GP vaccine, we generated a GFPDL containing 50- to 1,000-bp fragments of the GP gene from the EBOV Mayinga strain (FIG. 9) or the homologous Kikwit strain (FIGS. 10A and 10B), with >107 unique phage clones. These were expected to display all possible linear and conformational epitopes. The GP sequence of Mayinga of 1976 differs from the Kikwit strain of 1995 used in the vaccine by only nine amino acids, whereas the Makona strain of 2014 differs from Mayinga by 20 amino acids (FIGS. 10A and 10B).

Sequencing of the EBOV GFPDL confirmed a random distribution of size and sequence of inserts that spanned the entire GP (FIG. 11). To ascertain that the antibody repertoire identified using the GFPDL approach represented both linear and conformational epitopes, we performed two independent experiments. First, a panel of EBOV-protective monoclonal antibodies (MAbs) was used to identify and confirm the potential of the EBOV GFPDL to map both linear and conformational antibody epitopes. This panel included 6D8 and 13F6, which are components of the MB-003 cocktail for treatment of EBOV infection (FIG. 12), and conformation-dependent cross-reactive neutralizing and protective human MAbs derived from EBOV survivors (Flyak, A. I. et al. Cell 164, 392-405, 2016) (FIGS. 13A13C). The consensus epitope sequences obtained through GFPDL analysis were similar to the footprints previously identified for the MB-003 MAbs (Davidson, E. et al. J. Virol. 89, 10982-10992, 2015; Murin, C. D. et al. PNAS 111, 17182-17187, 2014) or for MAbs from survivors (Flyak, A. I. et al. Cell 164, 392-405, 2016), providing proof of concept that the GFPDL approach can identify linear and conformation-specific antibodies in polyclonal serum after EBOV infection or vaccination.

Second, we determined the capacity of the EBOV GFPDL to adsorb EBOV GP-specific antibodies in post-vaccination polyclonal human sera. After two rounds of adsorption with the EBOV GFPDL, 85-92% of GP-specific antibodies in post-vaccination human sera were adsorbed by GP phage display libraries, as determined by binding to EBOV GP in ELISA (FIG. 14). Together, the epitope mapping of MAbs and adsorption studies in post-vaccination polyclonal sera provided support for using the EBOV GP GFPDL to dissect the polyclonal antibody repertoires in human sera.

To study antibody responses after rVSVΔG-ZEBOV-GP vaccination, we collected serum specimens from individuals vaccinated with 3 million, 20 million or 100 million PFU vaccine or placebo control before vaccination (day 0), 28 d (day 28) after the primary vaccination and 28 d after booster vaccination (day 56). The sera of all participants in each dose group were pooled and used for mapping of overall antibody epitope repertoires by EBOV GFPDL (FIG. 1).

Prevaccination sera and the placebo controls were bound by very few phages. In the rVSVΔG-ZEBOV-GP-vaccinated groups, 4 weeks after the first vaccination, the number of bound phages was higher in sera from the 20-million-PFU dose (2.12×10⁶) group than in sera from the 3-million-PFU and 100-million-PFU groups (1.12×10⁶ and 1.45×10⁶ phages, respectively) (FIG. 1a ). Sequencing of GP fragments expressed by phages bound with sera after the first vaccination showed a high frequency of bound phages displaying both small and large fragments mapping across the N-terminal GP1 head domain and, to a lesser degree, the C-terminal GP2 stalk domain of the EBOV GP protein (FIG. 1b ). Sera from the 3-million-PFU and 20-million-PFU cohorts contained antibodies that mapped to the glycan cap and mucin domain and that recognized an epitope in the transmembrane region of the GP2 protein that was not captured by sera from the 100-million-PFU dose cohort. Sera from the 20-million-PFU dosing cohort additionally recognized several small and large immunodominant epitopes in the N-terminal half of EBOV GP mapping to the receptor-binding region (RBR) and between the RBR and the glycan cap domain (FIG. 1b ).

Unexpectedly, after the second vaccination, the number of EBOV GFPDL bound phages decreased 2-10 times relatively to the first vaccination (FIG. 1a ). The antibody epitope profiles did not substantially change, apart from an apparent reduction in antibodies mapping to the GP2 transmembrane region in the 3-million- and 20-million-PFU dose recipients, an increase in antibodies specific to the glycan cap in the 20-million-PFU cohort, and a small reduction in antibodies recognizing large sequences in the mucin-like domain from the 100-million-PFU group (FIG. 1c ).

Antigenic Sites within EBOV GP

EBOV-neutralizing and/or protective MAbs, such as KZ52 and the MAb cocktails ZMAb, ZMapp and MB-003, have been shown to recognize epitopes within or flanking the mucin-like domain, glycan cap or base of GP (Davidson, E. et al. J. Virol. 89, 10982-10992, 2015; Murin, C. D. et al. PNAS 111, 17182-17187, 2014) (FIG. 2a ). Vaccination with rVSVΔG-ZEBOV-GP generated an immune response to 19 unique antigenic sites defined by six large antigenic regions (herein referred to as GP-I through GP-VI) and 13 smaller antigenic sites (GP-II.1 through GP-V.7) contained within EBOV GP (FIG. 2a and FIGS. 6A and 6B). These antigenic regions and sites include several novel linear and conformational epitopes, including GP-II, GP-II.1, GP-II.2, GP-IV.1, GP-IV.3, GP-V.1, GP-V.4, GP-V.5, GP-V.6, GP-V.7 and an immunodominant sequence (GP-VI) in the transmembrane or cytoplasmic tail. The frequency of phages expressing these GP antigenic sites selected by sera after the first (FIG. 2b ) and second (FIG. 2c ) vaccinations for the three rVSVΔG-ZEBOV-GP dose groups are shown in FIGS. 6A and 6B. Antibodies in post-vaccination sera from the 20-million-PFU dose group showed the highest epitope diversity, as assessed by selecting phage clones from most of the antigenic sites within GP, whereas the sera from the lower (3 million PFU) and higher (100 million PFU) dose groups contained antibodies that predominantly mapped to the C-terminal half of the EBOV GP. The surface exposure of each of these antigenic sites on the EBOV GP crystal structure (Lee, J. E. et al. Nature 454, 177-182, 2008) (PDB 3CSY; includes GP residues 33-189, 214-278, 299-310 and 502-599) and the model of complete EBOV GP monomer (Yang, J. et al. Nat. Methods 12, 7-8, 2015) (FIG. 15) are shown in FIG. 3. The surface representation showed that most of the key antibody targets of rVSVΔG-ZEBOV-GP, including several of the GP epitopes (GP-II, GP-II.1, GP-II.2, GP-IV.1, GP-IV.3, GP-V.1, GP-V.4, GP-V.5, GP-V.6, GP-V.7) discovered in this study, are exposed on the native ZEBOV GP structures. Analysis of sequence homology of GP showed that some sites, including GP-II, GP-II.1, GP-IV.1, GP-IV.2 and GP-VI, are >70% conserved between diverse EBOV strains, such as Sudan, Bundibugyo, and Kikwit (FIG. 7). These data suggest that antibodies induced after rVSVΔG-ZEBOV-GP vaccination against some conserved antigenic sites may cross-react with diverse EBOV strains, even though cross-protection has not been observed in rVSVΔG-ZEBOVGP-vaccinated NHPs challenged with EBOV Sudan virus29.

Correlation of GP antibody binding with EBOV neutralization

Because the GFPDL analyses were carried out on the pooled serum samples from each group, we performed quantitative and qualitative analyses of individual pre- and post-vaccination sera with recombinant glycosylated GP produced in a mammalian system using an SPR-based real-time kinetics assay.

Binding kinetics of individual serum samples from the three vaccine-dose cohorts at early post-vaccination time points (28 d after first vaccination and 14 and 28 d after second vaccination) and at later time points (day 84 and day 180) was performed using the GP from Mayinga and Makona strains (FIG. 4a,b ). Antibody binding titers of individual serum samples (N=10 for each vaccine group at each time point) against GP were measured as resonance units (RU) in SPR (FIG. 4). Control sera from placebo did not show significant antibody binding to GP before or after mock vaccination. After the first rVSVΔG-ZEBOV-GP vaccination (day 28), all samples reacted strongly with GP from Mayinga (FIG. 4a ) and Makona strains (FIG. 4b ), with sera from the 20-million- and 100-million-PFU groups showing higher binding (mean RU=2,152 and 2,056, respectively) than those of the 3-million-PFU group (mean RU=1,197), but the difference among groups did not reach statistical significance. However, the mean serum antibody reactivity decreased marginally (mean RU=800 for 3 million PFU; 1,608 for 20 million PFU; 1,715 for 100 million PFU) for all the vaccine dose groups by day 42 (14 d after the second vaccination) and even further by day 56 (28 d after administration of the homologous boost; mean RU=679 for 3 million PFU; 1,409 for 20 million PFU; 1,536 for 100 million PFU). By days 84 and 180, serum anti-GP titers had diminished substantially, such that by day 180, 80% of individuals had very weak GP-binding antibody levels for all vaccine groups, though binding-antibody titers were marginally higher for the group that received the highest vaccine dose (mean GP binding RU=133 for 3 million PFU; 260 for 20 million PFU; 490 for 100 million PFU). We observed a strong correlation between in vitro EBOV neutralization titers (FIG. 4c ) and the titers of serum GP-binding antibody, as measured by SPR, after rVSVΔG-ZEBOV-GP vaccination (r=0.75; P<0.0001) (FIG. 4d ). This analysis revealed that the replicating rVSVΔG-ZEBOV-GP vaccination generated strong GP-binding antibodies that peaked after the first vaccination but were not boosted after the second vaccination and were not long lasting.

Antibody Affinity Maturation after Vaccination

To further investigate whether different rVSVΔG-ZEBOV-GP vaccine doses promote anti-GP affinity maturation, we determined the dissociation rates (Kd) of post-vaccination serum antibody-antigen complexes using SPR. Dissociation rate is independent of antibody concentration and provides a measurement of overall affinity of polyclonal antibody binding, as previously described (Khurana, S. et al. Sci. Transl. Med. 3, 85ra48, 2011). The off-rates for polyclonal serum antibodies bound to GP were lower (indicating stronger affinity) at 14 d and 28 d after the second vaccination than at 28 d after the first vaccination, but this difference reached statistical significance only for the 20-million-PFU and 100-million-PFU groups (FIG. 4c ). However, polyclonal antibody off-rates (Kd=10⁻²-10⁻³/s) were low, even after two vaccinations, compared to some other human viral vaccines (Khurana, S. et al. Sci. Transl. Med. 3, 85ra48, 2011). GP-specific antibody off-rates after the first (day 28) and second vaccination (day 56) correlated strongly with virus neutralization titers (r=−0.876, P=<0.0001), emphasizing the potential importance of antibody affinity maturation for antiviral activity (FIG. 4f ). These observations suggest that the higher rVSVΔG-ZEBOV-GP vaccine doses (20 million PFU and 100 million PFU) promote better antibody affinity maturation to GP than the lower vaccine dose.

Anti-GP Isotype and EBOV-Neutralizing Capacity

Isotype analysis of the GP-binding antibodies demonstrated representation of all isotypes (IgA, IgG and IgM) and IgG subclasses in postvaccination sera (FIG. 5a ). We were surprised to find that most of the GP-binding antibodies both after primary and after booster vaccinations, were of IgM isotype in all vaccine-dose groups (FIG. 5a ). The second most abundant GP-binding antibodies were of IgA isotype, and their frequency in serum increased with dosage (mean IgA=4% for 3 million PFU; 10% for 20 million PFU; 20% for 100 million PFU) at day 56. The anti-GP isotype reactivity was also analyzed by ELISA (FIGS. 16A-16C). Antibody isotyping of GP-binding antibodies in post-vaccination sera by ELISA showed concordance with the isotypes determined by SPR, but ELISA underestimated the proportion of GP-binding IgM antibodies compared to SPR. In contrast, at later time points (day 84 and day 180) after vaccination, the GP-binding antibodies remaining in the sera (FIG. 4a ) were of IgA or IgG subclasses (FIG. 5a ), suggesting that most of the anti-GP antibody response generated early after vaccination is of the IgM isotype, which does not provide a long-lasting systemic anti-GP antibody response. After vaccination, of the total GP-bound IgG antibodies, IgG1, IgG2 and IgG3 contributed most to GP binding in the 3-million-PFU and 20-million-PFU vaccine cohort, whereas for the 100-million-PFU dose a significant amount of anti-GP antibodies were of IgG3 and IgG4 subclasses (FIG. 17).

To understand the functional role of IgM antibodies in the postvaccination response, we evaluated their contribution to virus neutralization and compared them to IgG antibodies in post-vaccination sera. We used anti-human IgG and anti-human IgM affinity chromatography columns to purify IgG and IgM antibodies from three sera samples, taken after the second vaccination, that showed similar amounts of GP-binding IgG and IgM antibodies and evaluated binding to the GP in SPR (FIG. 5b ), isotype specificity (FIG. 5c,d ) and virus neutralization of Kikwit and Makona EBOV strains (FIG. 5e,f ). The IgG/IgM ratio determined from affinity chromatography in post-vaccination sera was in good agreement with that determined by SPR. The purified IgG and IgM antibodies from all sera reacted with GP, and, as expected, the IgG antibodies showed higher affinity (slower dissociation) to GP than IgM in SPR (FIG. 5b ). The purity of antibody isotypes was confirmed by human IgG- and human IgM-specific secondary antibodies using SPR (FIG. 5c,d ). The purified post-vaccination IgM antibodies at serum concentration levels contributed 40-50% to virus neutralization, and these results were similar to those with IgG antibodies purified from post-vaccination sera from the same individuals (FIGS. 5E and 5F). These results suggest that anti-GP IgM antibodies could have an important role in protection against EBOV disease in vivo.

The results of our study demonstrate independent evolution of antibody binding patterns to EBOV GP—in terms of epitope repertoire diversity, affinity maturation and isotype switching—in the three vaccine-dose groups after the first and second vaccinations and show an important contribution of anti-GP IgM antibodies to EBOV neutralization.

Discussion

In-depth understanding of the humoral immune response to Ebola vaccines under advanced development is required to identify meaningful correlates of protection in humans and animal models to facilitate evaluation of effective vaccine candidates. The epitope-binding patterns in the GP antigenic sites were most diverse in the 20-million-PFU dose samples. This effect, in which a more diverse antibody repertoire is generated from a lower vaccine dose, has been observed in multiple human influenza vaccination studies and was linked with optimal CD4+ T cell help, which may affect the B cell and T cell response differently after vaccination (Chung, K. Y. et al. Vaccine 33, 3953-3962, 2015; Nicholson, K. G. et al. Lancet 357, 1937-1943, 2001; Jackson, L. A. et al. J. Am. Med. Assoc. 314, 237-246, 2015; and Mulligan, M. J. et al. J. Am. Med. Assoc. 312, 1409-1419, 2014). The lower numbers of captured GFPDL phages after the second vaccination, as compared to the first vaccination, suggest that pre-existing antibodies against rVSVΔG-ZEBOV-GP after the first vaccination may have impeded replication of the rVSV vector and possibly masked some GP epitopes. Notably, the 20-million-PFU dose, selected for the phase 2/3 clinical trials in Western Africa on the basis of safety and in vitro neutralization data, generated the broadest antibody repertoire after vaccination.

After finding that a substantial proportion of anti-GP antibodies were of IgM and IgA isotypes, we performed GFPDL analysis to determine specific epitopes recognized by IgA, IgG and IgM antibodies in post-vaccination sera. In the sera pooled from each group after the first vaccination, the number of bound phages was approximately twofold higher in IgM-bound antibodies than in protein A/G-bound (primarily IgG) antibodies, and in IgA-bound antibodies was about tenfold lower for all vaccine groups (FIG. 8). We performed an additional analysis of sera from individuals in the 20-million-PFU and 100-million-PFU groups using IgA-, IgG- and IgM-specific capture beads to further define the fine epitope specificity of these antibodies after the first vaccination using homologous Kikwit GP EBOV strain GFPDL (FIGS. 18A-18C). The epitope repertoires of IgG-specific antibodies in individual post-vaccination sera were similar to those identified in IgG antibodies from pooled post-vaccination sera from the 20-million-PFU and 100-million-PFU dose groups (FIG. 1). However, the IgM antibody epitope repertoire in the 100-million-PFU dose group was more diverse than that of the 20-million-PFU group, which predominantly recognized the mucin-like domain. The individual IgM GFPDL responses quantitatively tracked the SPR data for total GP-binding antibodies, which measures binding of all anti-GP antibody isotypes. In both dose groups (20 million and 100 million PFU), IgA-specific polyclonal repertoire was more focused on the glycan cap and mucinlike domain, but sera from the 20-million-PFU group recognized the antigenic site V.7 at the C terminus of GP1 with higher frequency (FIGS. 18A-18C). One possible limitation of GFPDL-based assessment is that it is unlikely to detect paratopic interactions that require post-translational modification or rare quaternary epitopes that cross GP protomers. However, 85-92% of anti-GP antibodies from post-vaccination sera were removed by adsorption with the EBOV GP GFPDL, supporting the use of the EBOV GP GFPDL for analyses of human sera, as has been observed with other viral antigens, including different influenza strains, respiratory syncytial virus (RSV) protein F (RSV-F) and heavily glycosylated RSV-G. Moreover, binding to properly folded glycosylated Ebola GP in SPR can overcome these limitations and provide additional insight into the post-vaccination anti-GP polyclonal antibody response. Real-time antibody kinetics of individual post-vaccination sera by SPR revealed several unexpected findings, including lack of impact of the second vaccination on anti-GP responses, a fast decay of anti-GP titers within 2 months after the second vaccination, limited antibody class switching and modest antibody affinity maturation.

The observation of low antibody class switching after rVSVΔGZEBOV-GP vaccination is notable. Our findings suggest that IgM antibodies are the predominant isotype and decayed rapidly after the first and second vaccination. Although IgM antibodies are of low affinity, their multivalency compensates for overall binding avidity and helps in virus neutralization. Therefore, IgM antibodies may contribute to protection against infection, which would explain the relatively rapid protection that has been described in NHP studies and the rVSVΔGZEBOV-GP ring vaccination study in Africa. The amount of IgA in most post-vaccination sera samples was too low to purify and perform a reproducible EBOV neutralization assay. IgA purified from sera from two vaccine recipients showed that GP-specific IgA antibodies can neutralize virus in vitro but to a lesser extent than IgM antibodies.

Most ELISAs used for evaluation of Ebola vaccines measure predominantly anti-GP IgG antibody titers, because they rely on anti-human IgG secondary antibodies. Such ELISA titers alone may underestimate the full spectrum of the vaccine-induced immune response. Although incorporating an anti-human IgM secondary antibody in the ELISA may help mitigate this deficiency, the washing steps involved in the ELISA process, which are important to reduce nonspecific binding, may elute most of the low-affinity IgM antibodies. In addition, anti-GP IgA antibodies may contribute to protection against EBOV infection and disease in vivo, especially at mucosal surfaces. In contrast, the SPR approach captures all antibody classes, including IgM, IgA and IgG, and is also more appropriate for maintaining the native structure of EBOV GP and preserving conformational epitopes.

Class switching and antibody affinity maturation require continuous signals from T cells in the form of cytokines and comigration of antigen specific follicular helper T cells and B cells into germinal centers in lymph nodes. The influence of pre-existing rVSVΔG-ZEBOV-GP-specific antibodies or anti-VSV vector responses at the time of the booster vaccination, with their attenuating effects on rVSV replication and masking of GP epitopes, could adversely affect the formation of germinal centers and prevent antibody class switching, affinity maturation and durable response, as observed in previous vaccine studies. A second vaccination or prime-boost with alternative vaccine platforms (including different VSV serotype vectors) could provide a meaningful increase in affinity maturation and a better immune response, as was observed in prime-boost H5N1 and H7 influenza vaccine studies in humans. In these studies, it was observed that a 3-month minimum interval between the first and second vaccine doses was required for optimal neutralizing-antibody response and antibody affinity maturation.

In summary, we have demonstrated independent evolution of antibody immune responses—in terms of antibody epitope repertoire diversity, affinity maturation, durability and isotype switching—after vaccination with a live rVSV vector—based vaccine in three vaccine-dose groups and revealed the importance of a predominantly anti-GP IgM response for EBOV neutralization. These findings could have significant implications for further development and evaluation of Ebola vaccines. Future Ebola vaccine studies should follow the rate of decay of anti-VSV antibodies to identify the time interval needed for a booster vaccination to generate optimal antibody affinity maturation and durable antibody responses. Our observations suggest that it is important to develop appropriate assays that can provide in-depth understanding of post-vaccination and postinfection antibody responses to help guide development and evaluation of effective Ebola countermeasures such as therapeutics and vaccines.

Methods

Sera samples and monoclonal antibodies. Monoclonal antibodies (MAbs) and recombinant EBOV GP used in this study were purchased from IBT Bioservices Inc. Cross-reactive conformation-dependent neutralizing and protective human MAb 289 and MAb 324 from EBOV survivors were obtained from J. Crowe24. Phase 1, double-blind, placebo-controlled, dose-escalation trials with staggered enrollment were designed across three dose levels as outlined in Regules et al. (N. Engl. J. Med. 376(4):330-341, 2017, available online Apr. 1, 2015). Briefly, the rVSVΔG-ZEBOV-GP vaccine consisting of the rVSV strain Indiana and the glycoprotein of the EBOV Kikwit 1995 strain replacing the gene encoding the VSV envelope glycoprotein was administered at 3 million, 20 million or 100 million PFU in the form of a 1-mL injection in the deltoid muscle of healthy adult men and women according to protocols approved by the institutional review board at the US National Institutes of Health NIAID site. Written informed consent was obtained from all the volunteers before enrollment. Within each dosing cohort, 10 received active vaccine and 3 received a saline placebo. Serum samples from each individual were collected before vaccination (day 0), after the first vaccination (day 28), after the second vaccination (days 42 and 56), and on day 84 and day 180 (ClinicalTrials.gov number NCT02280408). Samples were anonymous, and permission to test these deidentified samples in different antibody assays was obtained from the US Food and Drug Administration's Research Involving Human Subjects Committee (FDA-RIHSC) under exemption protocol #15-0B; all assays done fell within the permissible usages in the original consent.

PsVN assay. Pseudovirion neutralization assay (PsVNA) against the homologous Zaire-Kikwit strain glycoprotein was performed as described previously (Regules, J. A. et al. N. Engl. J. Med. 376(4):330-341, 2017, available online Apr. 1, 2015).

GFPDL construction. cDNAs complementary to the envelope glycoprotein—encoding gene of EBOV Mayinga or Kikwit strain were chemically synthesized and used for cloning. A gIII display-based phage vector, fSK-9-3, where the desired polypeptide can be displayed on the surface of the phage as a gIII-fusion protein, was used. Purified DNA containing Ebola GP was digested with DNase I to obtain gene fragments of 50-1,000 bp and used for GFPDL construction as described previously (Khurana, S. et al. PLoS Med. 6, e1000049, 2009; Khurana, S. et al. Sci. Transl. Med. 3, 85ra48, 2011). As the phage libraries were constructed from the whole gene, they potentially display all possible known or unknown viral protein segments ranging in size from 15 to 350 amino acids as fusion proteins on the surface of the bacteriophage.

Adsorption of polyclonal human sera on EBOV GFPDL phages and residual reactivity to EBOV GP. Prior to panning of GFPDL, 500 □l tenfold-diluted serum antibodies from post-vaccination pooled human sera (n=10 each from the 20-million-PFU and 100-million-PFU groups; 5 μl serum from each vaccine to obtain a tenfold dilution for the pooled sera) were adsorbed by incubation in EBOV GFPDL phage-coated petri dishes. To ascertain residual antibody specificity, an ELISA was performed in wells coated with 200 ng/100 μl recombinant EBOV GP. After blocking with 20 mM PBS, pH 7.4, containing 0.05% Tween-20 (PBST) containing 2% milk, serial dilutions of human serum (with or without adsorption) in blocking solution were added to each well and incubated for 1 h at room temperature (RT) before addition of 5,000-fold diluted HRP-conjugated goat anti-human IgA⁺ IgG⁺ IgM antibody and developed by 100 μl o-phenylenediamine dihydrochloride (OPD) substrate solution. Absorbance was measured at 490 nm.

Affinity selection of EBOV GP GFPDL phages with rVSVΔG-ZEBOV-GP post-vaccination polyclonal human sera. Prior to panning of GFPDL with polyclonal serum antibodies, serum components that could nonspecifically interact with phage proteins were removed by incubation in UV-killed M13K07 phage-coated petri dishes. Equal volumes of pooled polyclonal human sera from each cohort were used for each round of GFPDL panning. All samples in each group (N=10) were pooled for GFPDL analysis. Subsequent GFPDL affinity selection was carried out in solution (with protein A/G) as previously described (Khurana, S. et al. PLoS Med. 6, e1000049, 2009; Khurana, S. et al. Sci. Transl. Med. 3, 85ra48, 2011). GFPDL affinity selection experiments were performed in quadruplicate (two independent experiments by two different investigators, who were blinded to sample identity) and showed similar numbers of phage clones and epitope repertoires. Additional antibody epitope repertoire analysis was performed using individual post-vaccination sera with similar neutralization titers from 20-million- and 100-million-PFU dose groups using IgA-, IgG- and IgM-specific capture beads to further define the fine epitope specificity of these antibodies in the individual sera using EBOV Kikwit GP GFPDL. A model for the complete Zaire strain GP generated using I-TASSER (Yang, J. et al. Nat. Methods 12, 7-8, 2015) was used to represent the antigenic sites on the structure. The crystal structure of Ebola GP (PDB 3CSY) was used as a reference (Lee, J. E. et al. Nature 454, 177-182, 2008).

Binding of rVSVΔG-ZEBOV-GP-vaccinated human sera to recombinant GP and off-rate measurements by surface plasmon resonance (SPR). Steadystate equilibrium binding of pre- and post-vaccination human polyclonal sera from every individual in the study was monitored at 25° C. using a ProteOn surface plasmon resonance (Bio-Rad). The purified recombinant GP was coupled to a GLC sensor chip via amine coupling with either 100 or 500 resonance units (RU) in the test flow channels. The protein density on the chip was optimized to measure only monovalent interactions independent of the antibody isotype. Samples of 300 μl freshly prepared sera at tenfold and 100-fold dilution BSAPBST buffer (PBS, pH 7.4, with Tween-20 and BSA) were injected at a flow rate of 50 μl/min (240 s contact duration) for association, and disassociation was performed over a 1,200-s interval. Responses from the protein surface were corrected for the response from a mock surface and for responses from a buffer-only injection. SPR was performed with serially diluted sera (tenfold and 100-fold dilutions) of each sample in this study such that the SPR signal of the samples between 5 to 100 RU was used for further quantitative analysis. The maximum resonance units (max RU) data were calculated by multiplying the observed RU signal with the dilution factor for each serum sample to provide the data for an undiluted serum sample. Antibody isotype analysis for the GP-bound antibodies in post-vaccination polyclonal sera was performed using SPR. Total antibody binding and isotype analysis were calculated with Bio-Rad ProteOn manager software (version 3.0.1). All SPR experiments were performed twice, and the researchers performing the assay were blinded to sample identity. In these optimized SPR conditions, the variation for each sample in duplicate SPR runs was <6%. Antibody off-rate constants, which describe the stability of the complex, i.e., the fraction of complexes decaying per second, were determined directly from the post-rVSVΔG-ZEBOV-GP-vaccination human polyclonal sera sample interaction with rGP protein using SPR (as described above) and calculated using the Bio-Rad ProteOn manager software for the heterogeneous sample model.

Purification of IgG and IgM antibodies from the post-vaccination sera. Fivefold-diluted post-second-vaccination sera were added to anti-human IgG or anti-human IgM immune-affinity resin and incubated for 1 h at RT on an end-to-end shaker before washing and purification of bound antibodies. The antibodies were eluted by 4 M magnesium chloride in 10 mM Tris (pH 7), followed by desalting. The purified IgG and IgM antibodies were normalized by volume to original serum concentrations and tested for GP binding then isotyped using anti-human IgG and anti-human IgM secondary antibodies in SPR to confirm the purity of each antibody isotype preparation. The purified IgG and IgM antibodies were subjected to virus microneutralization assay.

Statistical analyses. The statistical significance of group differences was determined by ordinary one-way ANOVA and Bonferroni's multiple-comparisons method. P<0.05 was considered significant with a 95% confidence interval. Correlations were calculated with the Pearson method, and P values for correlation were calculated by two-tailed test.

Data availability. The data sets generated during and/or analyzed during the study are available from the corresponding author upon reasonable request.

Example 2

This example demonstrates that immunization of rabbits and mice with selected peptide fragments conjugated to the carrier protein, keyhole limpet hemocyanin (KLH), generates strong binding antibodies against the matched Zaire ebolavirus and protects against ebolavirus infection.

An alignment of the glycoprotein (GP) amino acid sequences of 6 species of ebolavirus (Mayinga (1976), Kikwit (1995), Makona (2014), Bundibugyo (2012), Sudan (2000), Tai Forest) and Marburg margburgvirus is provided in FIGS. 19A-19C. Antigenic sites of ebolavirus GP as described herein are reflected in the table shown in FIG. 20, which shows the sequence of the antigenic site sin the context of the Zaire ebolavirus Mayinga GP sequence set forth as SEQ ID NO: 35.

Peptide fragment conjugation to KLH carrier protein: The conjugation procedure followed for peptide conjugation to Maleimide Activated mcKLH was performed as described in the product manual of Imject® Maleimide Activated mcKLH (Product 77605, Thermo Scientific). Several different fragments of SEQ ID NO: 35 were conjugated to the mcKLH.

Rabbit Immunization Studies:

Female New Zealand white rabbits were immunized three times intra-muscularly at 21-days interval with 25 micrograms of KLH conjugated peptides. Sera was collected before (pre-vaccination) and after 3rd vaccination and analyzed for binding antibodies using Surface Plasmon Resonance (SPR) and neutralization assay.

Binding of glycoprotein (GP) peptide vaccinated rabbit sera to different EBOV GP's and cross-reactivity measurements by Surface Plasmon Resonance (SPR): Steady-state equilibrium binding of pre- and post-KLH-GP vaccinated rabbit polyclonal sera from every rabbit was monitored at 25 degrees Celsius using a ProteOn surface plasmon resonance (Bio Rad). The purified GP were coupled to a GLC sensor chip via amine coupling with 500 resonance units (RU) in the test flow channels. The protein density on the chip was optimized such as to measure only monovalent interactions. Samples of 300 microliters of freshly prepared sera at 10-fold dilution in BSA-PBST buffer (PBS pH 7.4 buffer with Tween-20 and BSA) were injected at a flow rate of 50 microliters/min (240 sec contact duration) for association, and disassociation was performed over a 1200-second interval. Responses from the protein surface were corrected for the response from a mock surface and for responses from a buffer-only injection. The resonance units (RU) data shown for each sera in FIG. 21 was the observed RU signal for each serum sample.

Pseudovirion neutralization (PsVN) Assay: Pseudovirion neutralization assay (PsVNA) against the homologous Zaire-Kikwit strain glycoprotein was performed as described previously (Regules, J. A. et al. N. Engl. J. Med. 376(4):330-341, 2017, available online Apr. 1, 2015)

Discussion: Immunization of rabbits with selected ebolavirus antigenic peptides generated strong binding antibodies against the matched Ebola virus strain. Some of the immunized rabbit sera also showed strong cross reactivity to diverse ebolavirus strains including Bundibugyo and the Makona strain from the recent 2014 epidemic in Western Africa as well as diverse Sudan virus.

Rabbit anti-GP peptide post-vaccination sera were analyzed for virus neutralization in the PsVNA against the Zaire Mayinga strain showed that five antigenic peptides generated neutralizing antibodies (anti-GP 335-364, GP 457-484, GP 469-498, GP 617-645 and GP 630-646) against the Mayinga (1976) strain. Two of these peptides from the carboxy terminus of GP (GP 617-645 and GP 630-646) upon rabbit immunization generated strong neutralizing titers when tested in the conventional BSL4 based wild type Ebola virus with end-point titers of 320 and 640. Results are shown in the following table:

Neutralization titers of anti-GP peptide Rabbit sera GP 457-484 GP 630-646 GP 335-364 GP 469-498 GP 617-645 Pseudovirus Neut- Mayinga 62.24 194.1 85 44.86 79.14 Wild type PRNT- Mayinga 40 640 40.00 40 320 Pseudovirus Neut- Kikwit 45 179 62 Pseudovirus Neut- Makona 38.74 84.14 41.04

These anti-peptide rabbit sera also showed cross-neutralization of the distinct Kikwit and 2014-Makona strain as well with C-terminal peptide (GP 630-646) immunized sera showing the highest cross-neutralization titers.

Additional immunization assays were performed as discussed above using the peptides shown in FIG. 22. Again, peptides from the C-terminus of GP (GP 282-305, GP 343-368 and GP 520-547) that elicited a neutralizing immune response.

These rabbit studies confirmed that these antigenic GP peptides are immunogenic when vaccinated into animals that bind diverse multiple ebolaviruses and five of these conserved peptides generated neutralizing antibodies that also cross-neutralized diverse ebolaviruses.

Mouse Immunization and Challenge Studies

In another experiment (depicted in FIG. 23), female BALB/C mice were immunized on days 0 and 29 intra-muscularly with 20 micrograms of a KLH conjugated peptide (peptide fragments comprising SEQ ID NO: 17, SEQ ID NO: 21, SEQ ID NO: 3, SEQ ID NO: 29, SEQ ID NO: 10), each KLH-conjugated peptide fragment was screened separately. Furthermore, Female BALB/C mice were also used to study immunization with a combination of peptide fragments, a total of 20 micrograms comprising 4 microgram of each of the five KLH conjugated peptides (peptide fragments comprising SEQ ID NO: 17, SEQ ID NO: 21, SEQ ID NO: 3, SEQ ID NO: 29, SEQ ID NO: 10), with 10 mice per group). As a control, mice were injected with 20 micrograms of KLH only, or a particle based vaccine (VRP) expressing full length Zaire EBOV GP.

At day 63, the mice were challenged with 100 pfu Zaire ebolavirus Immunization with peptides from antigenic sites V.7 (SEQ ID NO: 3) and VI (SEQ ID NO: 10) induced sterilizing immunity to the viral challenge (FIG. 23), and protected against weight loss (FIG. 24).

Following immunization but prior to the viral challenge, sera was collected to assess the specificity of the immune response by surface plasmon resonance. As shown in FIG. 25, the conserved antigenic sites in the C-terminal region of GP1 and GP2 generate strong binding antibodies to both Mayinga and Makona GP.

Characterization of Human Sera from Ebolavirus Survivors

Additional assays were performed to determine if sera from subjects previously infected with Zaire ebolavirus targeted peptides corresponding to the antigenic sites identified herein (FIG. 26-27). Sera from infected human subjects targeted several of the identified sites, some of which strongly correlated with ebolavirus neutralization titers. The spatial structure of several of these sites is shown in FIG. 28

It will be apparent that the precise details of the methods or compositions described may be varied or modified without departing from the spirit of the described embodiments. We claim all such modifications and variations that fall within the scope and spirit of the claims below. 

It is claimed:
 1. A method for generating an immune response to ebolavirus GP in a subject, wherein the immune response inhibits or treats an ebolavirus infection, comprising selecting a subject with or at risk of an ebolavirus infection and administering to the subject an effective amount of a peptide to generate the immune response, wherein the peptide consists of or consists essentially of the antigenic site VI amino acid sequence set forth as any one: SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 and SEQ ID NO:
 53. 2. The method of claim 1, wherein the ebolavirus is selected from any one of Zaire ebolavirus, Bundibugyo ebolavirus, Sudan ebolavirus, or Tai Forest ebolavirus.
 3. The method of claim 1, wherein the peptide is linked to a heterologous carrier.
 4. The method of claim 3, wherein the peptide is linked to the carrier by a linker.
 5. The method of claim 3, wherein the carrier is a heterologous protein and the peptide is linked to the heterologous protein via a peptide linker to form a fusion protein.
 6. The method of claim 3, wherein the carrier comprises Keyhole Limpet Hemocyanin (KLH), Concholepas Concholepas Hemocyanin (CCH), Ovalbumin (OVA), bovine serum albumin, recombinant B. anthracis protective antigen, recombinant P. aeruginosa exotoxin A, tetanus toxoid, tetanus toxin heavy chain C fragment, diphtheria toxoid, diphtheria toxin variant CRM197, pertussis toxoid, H influenza protein D (HiD), recombinant Clostridium difficile toxin B subunit (rBRU), C. perfringens toxoid, or analogs or mimetics of and combinations of two or more thereof.
 7. The method of claim 6, wherein the carrier is Keyhole Limpet Hemocyanin (KLH).
 8. The method of claim 1, wherein the peptide consists of or consists essentially of the antigenic site VI amino acid sequence set forth as SEQ ID NO:
 10. 9. A method for generating an immune response to ebolavirus GP in a subject, comprising administering to the subject an effective amount of a peptide to generate the immune response wherein the peptide consists of or consists essentially of the antigenic site VI amino acid sequence set forth as SEQ ID NO:
 10. 10. The method of claim 1, wherein the peptide consists of or consists essentially of the antigenic site VI amino acid sequence set forth as SEQ ID NO:
 11. 11. The method of claim 1, wherein the peptide consists of or consists essentially of the antigenic site VI amino acid sequence set forth as SEQ ID NO:
 12. 12. The method of claim 1, wherein the peptide consists of or consists essentially of the antigenic site VI amino acid sequence set forth as SEQ ID NO:
 13. 13. The method of claim 1, wherein the peptide consists of or consists essentially of the antigenic site VI amino acid sequence set forth as SEQ ID NO:
 53. 